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operations "EDAM operations"Nandini BadarinarayanEDAM editors: Jon Ison, Matus Kalas, and Herve Menager. Contributors: Inge Jonassen, Dan Bolser, Hamish McWilliam, Mahmut Uludag, James Malone, Rodrigo Lopez, Steve Pettifer, and Peter Rice. Contibutions from these projects: EMBRACE, ELIXIR, and BioMedBridges (EU); EMBOSS (BBSRC, UK); eSysbio, FUGE Bioinformatics Platform, and ELIXIR.NO/Norwegian Bioinformatics Platform (Research Council of Norway). See http://edamontology.org for documentation and licence.concept_properties "EDAM concept properties"Andy BrownJames Maloneedam "EDAM"EDAM is an ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. EDAM is a simple ontology - essentially a set of terms with synonyms and definitions - organised into an intuitive hierarchy for convenient use by curators, software developers and end-users. EDAM is suitable for large-scale semantic annotations and categorisation of diverse bioinformatics resources. EDAM is also suitable for diverse application including for example within workbenches and workflow-management systems, software distributions, and resource registries.application/rdf+xmlrelations "EDAM relations"EDAM_topic http://edamontology.org/topic_ "EDAM topics"Jon IsonMatúš Kalaš1.16Duncan Hulldata "EDAM types of data"0.4Bioinformatics operations, data types, formats, identifiers and topicsJon Ison, Matus Kalas, Hervé MénagerEDAM1.6formats "EDAM data formats"Robert StevensHervé MénagerSWO and EDAM include some terms released under CC-BY license from the OBO Foundry. We acknowledge those with the use of the OBO PURLs were appropriate. Some of the definitions have been modified from the original; for the latest original definition please visit the URI. The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains SWO-specific classes and axioms as well as imported information from a variety of sources including OBI, IAO, BFO and EDAM. Please note that EDAM is imported as a whole and as such, some comments in the ontology header directly relate to EDAM only.EDAM http://edamontology.org/ "EDAM relations and concept properties"topics "EDAM topics"Helen Parkinson31.10.2016 23:58 GMTEDAM_operation http://edamontology.org/operation_ "EDAM operations"Allyson ListerDate of release: 1 February 20173791identifiers "EDAM types of identifiers"EDAM_format http://edamontology.org/format_ "EDAM data formats"EDAM_data http://edamontology.org/data_ "EDAM types of data"CitationPublicationPublication reference1.13trueconcept_properties'Citation' concept property ('citation' metadata tag) contains a dereferenceable URI, preferrably including a DOI, pointing to a citeable publication of the given data format.Created inVersion in which a concept was created.concept_propertiestrueDocumentation'Documentation' trailing modifier (qualifier, 'documentation') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to a page with explanation, description, documentation, or specification of the given data format.trueconcept_propertiesSpecificationExampletrue'Example' concept property ('example' metadata tag) lists examples of valid values of types of identifiers (accessions). Applicable to some other types of data, too.concept_propertiesSeparated by bar ('|'). For more complex data and data formats, it can be a link to a website with examples, instead.File extensionOntology used'File extension' concept property ('file_extension' metadata tag) lists examples of usual file extensions of formats.Separated by bar ('|'), without a dot ('.') prefix, preferrably not all capital characters.trueconcept_propertiesN.B.: File extensions that are not correspondigly defined at http://filext.com are recorded in EDAM only if not in conflict with http://filext.com, and/or unique and usual within life-science computing.'Ontology used' concept property ('ontology_used' metadata tag) of format concepts links to a domain ontology that is used inside the given data format, or contains a note about ontology use within the format.isdebtagconcept_propertiestrueWhen 'true', the concept has been proposed or is supported within Debian as a tag.Media typeconcept_propertiestrueMIME type'Media type' trailing modifier (qualifier, 'media_type') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to a page specifying a media type of the given data format.Obsolete sinceconcept_propertiesVersion in which a concept was made obsolete.trueOrganisationtrueconcept_propertiesOrganization'Organisation' trailing modifier (qualifier, 'organisation') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to an organisation that developed, standardised, and maintains the given data format.Regular expressionconcept_properties'Regular expression' concept property ('regex' metadata tag) specifies the allowed values of types of identifiers (accessions). Applicable to some other types of data, too.trueexample of usageA phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not.IAOdefinitiondefinitionalternative termdefinition sourcedefinition sourceobsoleted in versionEFO Development TeamThe version in which a class or property has been made obsoletereason for obsolescenceEFO Development TeamThe reason a class or property was made obsoleteSWO definitiondeprecatedis about'is about' relates an information entity to other entities in which the information entity holds some information which dscribes some facet of the other entity, such as the arrow direction on a sign.IAOJames MaloneAlan Ruttenbergpreceded byPlease note that, as stated on one of the RO documentation pages (https://code.google.com/p/obo-relations/wiki/ROAndBFO), some of the relations RO makes use are either uncontroversial (non-temporalized) parts of BFO2, or will be incorporated in the future. In the case of BFO_0000063, it is not currently in BFO2, but may be in the future. The RO ontologists assume this is the transitive form. For a full definition, refer to the inverse of this property, BFO_0000060. (Allyson Lister)OBO Foundryfollowed byModified by Allyson Lister from the preceded_by (which is the inverse of precedes / 'followed by') definition within RO: http://www.obofoundry.org/ro/ro.owlPlease note that, as stated on one of the RO documentation pages (https://code.google.com/p/obo-relations/wiki/ROAndBFO), some of the relations RO makes use are either uncontroversial (non-temporalized) parts of BFO2, or will be incorporated in the future. In the case of BFO_0000060, it is not currently in BFO2, but may be in the future. The RO ontologists assume this is the transitive form. (Allyson Lister)The assertion P 'followed by' P1 tells us something about Ps in general: that is, it tells us something about what happened later, given what we know about what happened earlier. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be preceded by some instance of P. Note that assertions using this property only are rather weak. Typically we will be interested in stronger relations, for example in the relation 'directly followed by'.OBO Foundryparticipates inAndy BrownPlease see the official RO definition for the inverse of this property, 'has participant.'has participantAndy BrownHas_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process.The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.http://obo-relations.googlecode.com/svn/trunk/src/ontology/core.owlinput ofAllyson ListerAn entity A is the 'input of' another entity B if A was put into the system, entity or software represented by B.output ofA piece of software can be the output of a particular software company via a software publishing process; data might be the output of a particular piece of data-producing software.Allyson ListerAn entity A is the 'output of' another entity B if it was produced as a result of the functioning of entity B.obsolete_is_published_byThe relationship between software and a software publisher.true0.5Marked as obsolete by Allyson Lister.This class can be entirely replaced with 'is published by', SWO_0004004. Please use SWO_0004004 instead.has legal status1.4Marked as obsolete by Allyson Lister.This property was not in use anywhere in the ontology. Further, it had no definition and therefore its intended usage was unclear. Until a time when this property is required and an official definition created, this property is obsolete so as not to introduce inconsistent usage.trueis encoded inAllyson ListerIs encoded in is an "is about" relationship which describes the type of encoding used for the referenced class.Linking a type of software to its particular programming language.has specified data inputSee also http://softwareontology.wordpress.com/2011/04/15/ins-and-outs-of-software/The relationship between input data which is permitted to a piece of software.James Malonehas specified data outputSee also http://softwareontology.wordpress.com/2011/04/15/ins-and-outs-of-software/James MaloneThe relationship between a piece of software and the data that it is possible to output.is specified data input ofThe relationship between a data and the software which can possibly take this data as input.James Maloneis specified data output ofThe relationship between a data and the software which can possibly produce this data as output.James Malonedirectly preceded byAllyson ListerEntity A is 'directly preceded by' entity B if there are no intermediate entities temporally between the two entities. WIthin SWO this property is mainly used to describe versions of entities such as software.Microsoft version 2007 is directly preceded by Microsoft version 2003.OBO Foundrydirectly followed by'directly followed by' is an object property which further specializes the parent 'followed by' property. In the assertion 'C directly followed by C1', says that Cs generally are immediately followed by C1s.Allyson Listerhas format specificationAllyson ListerHas format specification is a type of "is encoded in" relationship which specifically describes the relationship between data and a data format specification.obsolete_is developed byJames Malonetrue0.3Marked as obsolete by Allyson Lister.is developed by and is_developed_by. The former is from the core file and originally had no identifier (though it is now identified via SWO_0004003), and the latter is from the original file (SWO_0000394). SWO_0000394 was retained and SWO_0004003 marked as obsolete as SWO_0004003 had no usages while SWO_0000394 has many usages. Finally, the underscores were removed from the label of SWO_0000394 so it would conform to our naming scheme. Please use SWO_0000394 instead.obsolete object propertyMarked as obsolete by Allyson ListerStores those object properties which are no longer appropriate for use within SWO.Allyson Listerobsolete_is specified output oftrueMarked as obsolete by Allyson Lister.There is an object property duplication for is specified output of, where one is from OBI (OBI_0000312) and one is from SWO (SWO_9000058); additionally, the reasoner infers these two object properties as equivalent. Both are the inverse properties for has specified output. It makes sense to retain the OBI object property. The SWO class URI was renamed to the OBI term URI (to make the moving of the axioms across to the OBI term simple), and then an SWO class with the original URI was marked as obsolete. Please use OBI_0000312 instead.0.3has clauseAllyson ListerAxioms using the 'has clause' property, e.g. C 'has clause' C1, provide links from the left hand class to the instances within the 'license clause' hierarchy. This provides a way to more precisely assert the constraints of the licensing applied.has licenseThe relationship between an entity and the set of legal restrictions, i.e. license, which are applied in using or otherwise interacting with that entity. Eg. relationship between software and a software license.is license forThe relationship between an entity and the set of legal restrictions, i.e. license, which are applied in using or otherwise interacting with that entity. Eg. relationship between a software license and the software which implements it.has declared status'has declared status' provides a way to assert the developmental status of a class, such as whether it is stable or under development. Is especially useful for software that might not be complete or stable yet, and when combined with version information.Allyson Listerobsolete_has_participant1.4Exact equivalence with RO class http://purl.obolibrary.org/obo/RO_0000057, to the extent that the inverse of RO_0000057 was already present in this ontology as the inverse of this SWO class.truehas download locationAllyson ListerThe location from where the software can be downloaded.Allyson Listerhas website homepagehas website homepageAllyson ListerThe URL of the homepage for the resource this property is associated with.Resource typeA type of computational resource used in bioinformatics.beta12orEarliertruebeta12orEarlierDataInformation, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output.Datumhttp://wsio.org/data_002http://www.ifomis.org/bfo/1.1/snap#ContinuantData sethttp://semanticscience.org/resource/SIO_000088beta12orEarlierhttp://semanticscience.org/resource/SIO_000069http://purl.org/biotop/biotop.owl#DigitalEntity"http://purl.obolibrary.org/obo/IAO_0000027"Data record"http://purl.obolibrary.org/obo/IAO_0000030"http://www.onto-med.de/ontologies/gfo.owl#PerpetuantData recordEDAM does not distinguish a data record (a tool-understandable information artefact) from data or datum (its content, the tool-understandable encoding of an information).EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set).Data setEDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set).DatumTooltruebeta12orEarlierbeta12orEarlierA bioinformatics package or tool, e.g. a standalone application or web service.Databasebeta12orEarliertruebeta12orEarlierA digital data archive typically based around a relational model but sometimes using an object-oriented, tree or graph-based model.Ontologybeta12orEarlierAn ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc.OntologiesDirectory metadata1.5A directory on disk from which files are read.truebeta12orEarlierMeSH vocabularybeta12orEarlierControlled vocabulary from National Library of Medicine. The MeSH thesaurus is used to index articles in biomedical journals for the Medline/PubMED databases.beta12orEarliertrueHGNC vocabularyControlled vocabulary for gene names (symbols) from HUGO Gene Nomenclature Committee.beta12orEarliertruebeta12orEarlierUMLS vocabularytruebeta12orEarlierCompendium of controlled vocabularies for the biomedical domain (Unified Medical Language System).beta12orEarlierIdentifierhttp://wsio.org/data_005IDbeta12orEarlierA text token, number or something else which identifies an entity, but which may not be persistent (stable) or unique (the same identifier may identify multiple things).http://semanticscience.org/resource/SIO_000115"http://purl.org/dc/elements/1.1/identifier"Almost exact but limited to identifying resources.Database entryAn entry (retrievable via URL) from a biological database.truebeta12orEarlierbeta12orEarlierMolecular massMass of a molecule.beta12orEarlierMolecular chargeNet charge of a molecule.PDBML:pdbx_formal_chargebeta12orEarlierChemical formulaA specification of a chemical structure.Chemical structure specificationbeta12orEarlierQSAR descriptorQSAR descriptors have numeric values that quantify chemical information encoded in a symbolic representation of a molecule. They are used in quantitative structure activity relationship (QSAR) applications. Many subtypes of individual descriptors (not included in EDAM) cover various types of protein properties.beta12orEarlierA QSAR quantitative descriptor (name-value pair) of chemical structure.Raw sequenceNon-sequence characters may be used for example for gaps and translation stop.A raw molecular sequence (string of characters) which might include ambiguity, unknown positions and non-sequence characters.beta12orEarlierSequence recordA molecular sequence and associated metadata.beta12orEarlierSO:2000061http://purl.bioontology.org/ontology/MSH/D058977Sequence setbeta12orEarlierA collection of multiple molecular sequences and associated metadata that do not (typically) correspond to molecular sequence database records or entries and which (typically) are derived from some analytical method.This concept may be used for arbitrary sequence sets and associated data arising from processing.SO:0001260Sequence mask character1.5truebeta12orEarlierA character used to replace (mask) other characters in a molecular sequence.Sequence mask type1.5Sequence masking is where specific characters or positions in a molecular sequence are masked (replaced) with an another (mask character). The mask type indicates what is masked, for example regions that are not of interest or which are information-poor including acidic protein regions, basic protein regions, proline-rich regions, low compositional complexity regions, short-periodicity internal repeats, simple repeats and low complexity regions. Masked sequences are used in database search to eliminate statistically significant but biologically uninteresting hits.beta12orEarliertrueA label (text token) describing the type of sequence masking to perform.DNA sense specificationbeta12orEarlierStrandThe strand of a DNA sequence (forward or reverse).DNA strand specificationThe forward or 'top' strand might specify a sequence is to be used as given, the reverse or 'bottom' strand specifying the reverse complement of the sequence is to be used.Sequence length specification1.5truebeta12orEarlierA specification of sequence length(s).Sequence metadatatrueBasic or general information concerning molecular sequences.beta12orEarlier1.5This is used for such things as a report including the sequence identifier, type and length.Sequence feature sourceHow the annotation of a sequence feature (for example in EMBL or Swiss-Prot) was derived.beta12orEarlierThis might be the name and version of a software tool, the name of a database, or 'curated' to indicate a manual annotation (made by a human).Sequence search resultsDatabase hits (sequence)The score list includes the alignment score, percentage of the query sequence matched, length of the database sequence entry in this alignment, identifier of the database sequence entry, excerpt of the database sequence entry description etc.Sequence database hitsSequence database search resultsbeta12orEarlierSequence search hitsA report of sequence hits and associated data from searching a database of sequences (for example a BLAST search). This will typically include a list of scores (often with statistical evaluation) and a set of alignments for the hits.Sequence signature matchesSequence profile matchesbeta12orEarlierReport on the location of matches in one or more sequences to profiles, motifs (conserved or functional patterns) or other signatures.Sequence motif matchesSearch results (protein secondary database)This ncluding reports of hits from a search of a protein secondary or domain database.Protein secondary database search resultsSequence signature modelbeta12orEarlierData files used by motif or profile methods.truebeta12orEarlierSequence signature dataThis can include metadata about a motif or sequence profile such as its name, length, technical details about the profile construction, and so on.beta12orEarlierData concering concerning specific or conserved pattern in molecular sequences and the classifiers used for their identification, including sequence motifs, profiles or other diagnostic element.Sequence alignment (words)Sequence word alignment1.5beta12orEarliertrueAlignment of exact matches between subsequences (words) within two or more molecular sequences.Dotplotbeta12orEarlierA dotplot of sequence similarities identified from word-matching or character comparison.Sequence alignmenthttp://semanticscience.org/resource/SIO_010066Alignment of multiple molecular sequences.http://purl.bioontology.org/ontology/MSH/D016415beta12orEarlierhttp://en.wikipedia.org/wiki/Sequence_alignmentSequence alignment parametertruebeta12orEarlier1.5Some simple value controlling a sequence alignment (or similar 'match') operation.Sequence similarity scoreA value representing molecular sequence similarity.beta12orEarlierSequence alignment metadatabeta12orEarliertrueReport of general information on a sequence alignment, typically include a description, sequence identifiers and alignment score.1.5Sequence alignment reportbeta12orEarlierUse this for any computer-generated reports on sequence alignments, and for general information (metadata) on a sequence alignment, such as a description, sequence identifiers and alignment score.An informative report of molecular sequence alignment-derived data or metadata.Profile-profile alignmentSequence profile alignmentA profile-profile alignment (each profile typically representing a sequence alignment).beta12orEarlierSequence-profile alignmentAlignment of one or more molecular sequence(s) to one or more sequence profile(s) (each profile typically representing a sequence alignment).beta12orEarlierData associated with the alignment might also be included, e.g. ranked list of best-scoring sequences and a graphical representation of scores.Sequence distance matrixA matrix of estimated evolutionary distance between molecular sequences, such as is suitable for phylogenetic tree calculation.Phylogenetic distance matrixMethods might perform character compatibility analysis or identify patterns of similarity in an alignment or data matrix.Moby:phylogenetic_distance_matrixbeta12orEarlierPhylogenetic character databeta12orEarlierBasic character data from which a phylogenetic tree may be generated.As defined, this concept would also include molecular sequences, microsatellites, polymorphisms (RAPDs, RFLPs, or AFLPs), restriction sites and fragmentshttp://www.evolutionaryontology.org/cdao.owl#CharacterPhylogenetic treeA phylogenetic tree is usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. See also 'Phylogenetic tree image'.The raw data (not just an image) from which a phylogenetic tree is directly generated or plotted, such as topology, lengths (in time or in expected amounts of variance) and a confidence interval for each length.Moby:phylogenetic_treePhylogenyMoby:Treehttp://www.evolutionaryontology.org/cdao.owl#TreeMoby:myTreebeta12orEarlierhttp://purl.bioontology.org/ontology/MSH/D010802Comparison matrixMatrix of integer or floating point numbers for amino acid or nucleotide sequence comparison.Substitution matrixbeta12orEarlierThe comparison matrix might include matrix name, optional comment, height and width (or size) of matrix, an index row/column (of characters) and data rows/columns (of integers or floats).Protein topologybeta12orEarliertrueThe location and size of the secondary structure elements and intervening loop regions is usually indicated.beta12orEarlierPredicted or actual protein topology represented as a string of protein secondary structure elements.Protein features report (secondary structure)1.8beta12orEarliertrueSecondary structure (predicted or real) of a protein.Protein features report (super-secondary)beta12orEarliertrueSuper-secondary structure of protein sequence(s).1.8Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc.Secondary structure alignment (protein)beta12orEarlierAlignment of the (1D representations of) secondary structure of two or more proteins.Secondary structure alignment metadata (protein)beta12orEarlierAn informative report on protein secondary structure alignment-derived data or metadata.beta12orEarliertrueRNA secondary structureThis includes thermodynamically stable or evolutionarily conserved structures such as knots, pseudoknots etc.Secondary structure (RNA)An informative report of secondary structure (predicted or real) of an RNA molecule.beta12orEarlierMoby:RNAStructMLSecondary structure alignment (RNA)Alignment of the (1D representations of) secondary structure of two or more RNA molecules.Moby:RNAStructAlignmentMLbeta12orEarlierSecondary structure alignment metadata (RNA)beta12orEarliertruebeta12orEarlierAn informative report of RNA secondary structure alignment-derived data or metadata.StructureCoordinate modelThe coordinate data may be predicted or real.http://purl.bioontology.org/ontology/MSH/D0153943D coordinate and associated data for a macromolecular tertiary (3D) structure or part of a structure.Structure databeta12orEarlierTertiary structure recordbeta12orEarlierbeta12orEarliertrueAn entry from a molecular tertiary (3D) structure database.Structure database search resultsResults (hits) from searching a database of tertiary structure.1.8truebeta12orEarlierStructure alignmentbeta12orEarlierA tertiary structure alignment will include the untransformed coordinates of one macromolecule, followed by the second (or subsequent) structure(s) with all the coordinates transformed (by rotation / translation) to give a superposition.Alignment (superimposition) of molecular tertiary (3D) structures.Structure alignment reportThis is a broad data type and is used a placeholder for other, more specific types.An informative report of molecular tertiary structure alignment-derived data.beta12orEarlierStructure similarity scorebeta12orEarlierA value representing molecular structure similarity, measured from structure alignment or some other type of structure comparison.Structural profileStructural (3D) profilebeta12orEarlier3D profileSome type of structural (3D) profile or template (representing a structure or structure alignment).Structural (3D) profile alignmentbeta12orEarlierA 3D profile-3D profile alignment (each profile representing structures or a structure alignment).Structural profile alignmentSequence-3D profile alignmentSequence-structural profile alignmentAn alignment of a sequence to a 3D profile (representing structures or a structure alignment).1.5truebeta12orEarlierProtein sequence-structure scoring matrixMatrix of values used for scoring sequence-structure compatibility.beta12orEarlierSequence-structure alignmentAn alignment of molecular sequence to structure (from threading sequence(s) through 3D structure or representation of structure(s)).beta12orEarlierAmino acid annotation1.4truebeta12orEarlierAn informative report about a specific amino acid.Peptide annotation1.4truebeta12orEarlierAn informative report about a specific peptide.Protein reportGene product annotationAn informative human-readable report about one or more specific protein molecules or protein structural domains, derived from analysis of primary (sequence or structural) data.beta12orEarlierProtein propertybeta12orEarlierA report of primarily non-positional data describing intrinsic physical, chemical or other properties of a protein molecule or model.Protein sequence statisticsThe report may be based on analysis of nucleic acid sequence or structural data. This is a broad data type and is used a placeholder for other, more specific types.Protein physicochemical propertyProtein propertiesProtein structural motifs and surfacesbeta12orEarliertrue3D structural motifs in a protein.1.8Protein domain classification1.5Data concerning the classification of the sequences and/or structures of protein structural domain(s).truebeta12orEarlierProtein features report (domains)structural domains or 3D folds in a protein or polypeptide chain.1.8truebeta12orEarlierProtein architecture report1.4truebeta12orEarlierAn informative report on architecture (spatial arrangement of secondary structure) of a protein structure.Protein folding report1.8A report on an analysis or model of protein folding properties, folding pathways, residues or sites that are key to protein folding, nucleation or stabilisation centers etc.truebeta12orEarlierProtein features (mutation)beta12orEarliertruebeta13This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.Data on the effect of (typically point) mutation on protein folding, stability, structure and function.Protein interaction raw dataThis is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.Protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc.beta12orEarlierProtein interaction reportProtein non-covalent interactions reportbeta12orEarlierAn informative report on interactions (predicted or known) within or between a protein, structural domain or part of a protein. This includes intra- and inter-residue contacts and distances, as well as interactions with other proteins and non-protein entities such as nucleic acid, metal atoms, water, ions etc.
Protein report (interaction)Atom interaction dataResidue interaction dataProtein interaction recordProtein family reportAn informative report on a specific protein family or other classification or group of protein sequences or structures.Protein family annotationProtein classification databeta12orEarlierVmaxThe maximum initial velocity or rate of a reaction. It is the limiting velocity as substrate concentrations get very large.beta12orEarlierKmbeta12orEarlierKm is the concentration (usually in Molar units) of substrate that leads to half-maximal velocity of an enzyme-catalysed reaction.Nucleotide base annotationbeta12orEarliertrue1.4An informative report about a specific nucleotide base.Nucleic acid propertyGC-contentThe report may be based on analysis of nucleic acid sequence or structural data. This is a broad data type and is used a placeholder for other, more specific types.A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a nucleic acid molecule.beta12orEarlierNucleic acid physicochemical propertyCodon usage dataThis is a broad data type and is used a placeholder for other, more specific types.beta12orEarlierData derived from analysis of codon usage (typically a codon usage table) of DNA sequences.Gene reportGene structure (repot)Moby_namespace:Human_Readable_DescriptionA report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc.Gene function (report)Nucleic acid features (gene and transcript structure)Moby:geneGene and transcript structure (report)beta12orEarlierGene annotationMoby:GeneInfoGene features reportThis includes any report on a particular locus or gene. This might include the gene name, description, summary and so on. It can include details about the function of a gene, such as its encoded protein or a functional classification of the gene sequence along according to the encoded protein(s).Gene classificationtruebeta12orEarlierbeta12orEarlierA report on the classification of nucleic acid / gene sequences according to the functional classification of their gene products.DNA variationstable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms.1.8truebeta12orEarlierChromosome reportAn informative report on a specific chromosome.This includes basic information. e.g. chromosome number, length, karyotype features, chromosome sequence etc.beta12orEarlierGenotype/phenotype reportGenotype/phenotype annotationAn informative report on the set of genes (or allelic forms) present in an individual, organism or cell and associated with a specific physical characteristic, or a report concerning an organisms traits and phenotypes.beta12orEarlierNucleic acid features report (primers)PCR primers and hybridisation oligos in a nucleic acid sequence.1.8truebeta12orEarlierPCR experiment report1.8PCR experiments, e.g. quantitative real-time PCR.truebeta12orEarlierSequence traceThis is the raw data produced by a DNA sequencing machine.beta12orEarlierFluorescence trace data generated by an automated DNA sequencer, which can be interprted as a molecular sequence (reads), given associated sequencing metadata such as base-call quality scores.Sequence assemblyAn assembly of fragments of a (typically genomic) DNA sequence.SO:0001248SO:0000353ContigsTypically, an assembly is a collection of contigs (for example ESTs and genomic DNA fragments) that are ordered, aligned and merged. Annotation of the assembled sequence might be included.beta12orEarlierhttp://en.wikipedia.org/wiki/Sequence_assemblySO:0001248Perhaps surprisingly, the definition of 'SO:assembly' is narrower than the 'SO:sequence_assembly'.Radiation Hybrid (RH) scoresbeta12orEarlierRadiation Hybrid (RH) scores are used in Radiation Hybrid mapping.Radiation hybrid scores (RH) scores for one or more markers.Genetic linkage reportLinkage disequilibrium (report)Gene annotation (linkage)This includes linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome).beta12orEarlierAn informative report on the linkage of alleles.Gene expression profilebeta12orEarlierGene expression patternData quantifying the level of expression of (typically) multiple genes, derived for example from microarray experiments.Microarray experiment report1.8truebeta12orEarliermicroarray experiments including conditions, protocol, sample:data relationships etc.Oligonucleotide probe databeta13beta12orEarliertrueData on oligonucleotide probes (typically for use with DNA microarrays).SAGE experimental databeta12orEarliertruebeta12orEarlierOutput from a serial analysis of gene expression (SAGE) experiment.MPSS experimental databeta12orEarlierbeta12orEarliertrueMassively parallel signature sequencing (MPSS) data.SBS experimental dataSequencing by synthesis (SBS) data.beta12orEarliertruebeta12orEarlierSequence tag profile (with gene assignment)Tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data. Typically this is the sequencing-based expression profile annotated with gene identifiers.1.14truebeta12orEarlierProtein X-ray crystallographic databeta12orEarlierX-ray crystallography data.Protein NMR databeta12orEarlierProtein nuclear magnetic resonance (NMR) raw data.Protein circular dichroism (CD) spectroscopic databeta12orEarlierProtein secondary structure from protein coordinate or circular dichroism (CD) spectroscopic data.Electron microscopy volume mapbeta12orEarlierVolume map data from electron microscopy.EM volume mapElectron microscopy modelbeta12orEarlierAnnotation on a structural 3D model (volume map) from electron microscopy.This might include the location in the model of the known features of a particular macromolecule.2D PAGE imageTwo-dimensional gel electrophoresis imagebeta12orEarlierMass spectrometry spectrabeta12orEarlierSpectra from mass spectrometry.Peptide mass fingerprintProtein fingerprintPeak listbeta12orEarlierA set of peptide masses (peptide mass fingerprint) from mass spectrometry.A molecular weight standard fingerprint is standard protonated molecular masses e.g. from trypsin (modified porcine trypsin, Promega) and keratin peptides.Molecular weights standard fingerprintPeptide identification'Protein identification'Protein or peptide identifications with evidence supporting the identifications, for example from comparing a peptide mass fingerprint (from mass spectrometry) to a sequence database, or the set of typical spectra one obtains when running a protein through a mass spectrometer.beta12orEarlierPathway or network annotationbeta12orEarlierbeta12orEarliertrueAn informative report about a specific biological pathway or network, typically including a map (diagram) of the pathway.Biological pathway mapbeta12orEarlierbeta12orEarlierA map (typically a diagram) of a biological pathway.trueData resource definitiontrueA definition of a data resource serving one or more types of data, including metadata and links to the resource or data proper.beta12orEarlier1.5Workflow metadataBasic information, annotation or documentation concerning a workflow (but not the workflow itself).beta12orEarlierMathematical modelbeta12orEarlierBiological modelA biological model represented in mathematical terms.Statistical estimate scoreA value representing estimated statistical significance of some observed data; typically sequence database hits.beta12orEarlierEMBOSS database resource definitionbeta12orEarliertrueResource definition for an EMBOSS database.1.5Version information1.5Development status / maturity may be part of the version information, for example in case of tools, standards, or some data records.Information on a version of software or data, for example name, version number and release date.truebeta12orEarlierDatabase cross-mappingThe cross-mapping is typically a table where each row is an accession number and each column is a database being cross-referenced. The cells give the accession number or identifier of the corresponding entry in a database. If a cell in the table is not filled then no mapping could be found for the database. Additional information might be given on version, date etc.beta12orEarlierA mapping of the accession numbers (or other database identifier) of entries between (typically) two biological or biomedical databases.Data indexbeta12orEarlierAn index of data of biological relevance.Data index reportDatabase index annotationbeta12orEarlierA report of an analysis of an index of biological data.Database metadatabeta12orEarlierBasic information on bioinformatics database(s) or other data sources such as name, type, description, URL etc.Tool metadatabeta12orEarlierBasic information about one or more bioinformatics applications or packages, such as name, type, description, or other documentation.Job metadatabeta12orEarliertrue1.5Textual metadata on a submitted or completed job.User metadatabeta12orEarlierTextual metadata on a software author or end-user, for example a person or other software.Small molecule reportSmall molecule annotationAn informative report on a specific chemical compound.Chemical compound annotationbeta12orEarlierChemical structure reportCell line reportbeta12orEarlierReport on a particular strain of organism cell line including plants, virus, fungi and bacteria. The data typically includes strain number, organism type, growth conditions, source and so on.Cell line annotationOrganism strain dataScent annotationAn informative report about a specific scent.1.4beta12orEarliertrueOntology termbeta12orEarlierOntology termsA term (name) from an ontology.Ontology class nameOntology concept dataOntology class metadatabeta12orEarlierOntology term metadataData concerning or derived from a concept from a biological ontology.Keywordbeta12orEarlierBoolean operators (AND, OR and NOT) and wildcard characters may be allowed.Keyword(s) or phrase(s) used (typically) for text-searching purposes.PhrasesMoby:Wildcard_QueryMoby:QueryStringMoby:BooleanQueryStringTermMoby:Global_KeywordCitationBibliographic referencebeta12orEarlierMoby:PublicationMoby:GCP_SimpleCitationReferenceBibliographic data that uniquely identifies a scientific article, book or other published material.A bibliographic reference might include information such as authors, title, journal name, date and (possibly) a link to the abstract or full-text of the article if available.ArticleArticle textbeta12orEarlierA scientific text, typically a full text article from a scientific journal.Scientific articleText mining reportbeta12orEarlierAn abstract of the results of text mining.Text mining outputA text mining abstract will typically include an annotated a list of words or sentences extracted from one or more scientific articles.Entity identifierbeta12orEarliertruebeta12orEarlierAn identifier of a biological entity or phenomenon.Data resource identifierbeta12orEarlierAn identifier of a data resource.truebeta12orEarlierIdentifier (typed)An identifier that identifies a particular type of data.beta12orEarlierThis concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'.Tool identifierbeta12orEarlierAn identifier of a bioinformatics tool, e.g. an application or web service.Discrete entity identifierbeta12orEarlierName or other identifier of a discrete entity (any biological thing with a distinct, discrete physical existence).beta12orEarliertrueEntity feature identifiertruebeta12orEarlierName or other identifier of an entity feature (a physical part or region of a discrete biological entity, or a feature that can be mapped to such a thing).beta12orEarlierEntity collection identifierbeta12orEarlierbeta12orEarliertrueName or other identifier of a collection of discrete biological entities.Phenomenon identifierbeta12orEarliertruebeta12orEarlierName or other identifier of a physical, observable biological occurrence or event.Molecule identifierbeta12orEarlierName or other identifier of a molecule.Atom IDbeta12orEarlierIdentifier (e.g. character symbol) of a specific atom.Atom identifierMolecule namebeta12orEarlierName of a specific molecule.Molecule typeFor example, 'Protein', 'DNA', 'RNA' etc.truebeta12orEarlierProtein|DNA|RNAA label (text token) describing the type a molecule.1.5Chemical identifierbeta12orEarlierUnique identifier of a chemical compound.truebeta12orEarlierChromosome nameName of a chromosome.beta12orEarlierPeptide identifierbeta12orEarlierIdentifier of a peptide chain.Protein identifierIdentifier of a protein.beta12orEarlierCompound nameUnique name of a chemical compound.Chemical namebeta12orEarlierChemical registry numberbeta12orEarlierUnique registry number of a chemical compound.Ligand identifiertruebeta12orEarlierCode word for a ligand, for example from a PDB file.beta12orEarlierDrug identifierIdentifier of a drug.beta12orEarlierAmino acid identifierbeta12orEarlierResidue identifierIdentifier of an amino acid.Nucleotide identifierName or other identifier of a nucleotide.beta12orEarlierMonosaccharide identifierIdentifier of a monosaccharide.beta12orEarlierChemical name (ChEBI)This is the recommended chemical name for use for example in database annotation.Unique name from Chemical Entities of Biological Interest (ChEBI) of a chemical compound.beta12orEarlierChEBI chemical nameChemical name (IUPAC)IUPAC chemical namebeta12orEarlierIUPAC recommended name of a chemical compound.Chemical name (INN)beta12orEarlierINN chemical nameInternational Non-proprietary Name (INN or 'generic name') of a chemical compound, assigned by the World Health Organisation (WHO).Chemical name (brand)Brand name of a chemical compound.beta12orEarlierBrand chemical nameChemical name (synonymous)Synonymous chemical nameSynonymous name of a chemical compound.beta12orEarlierChemical registry number (CAS)CAS registry number of a chemical compound.beta12orEarlierCAS chemical registry numberChemical registry number (Beilstein)Beilstein registry number of a chemical compound.beta12orEarlierBeilstein chemical registry numberChemical registry number (Gmelin)Gmelin registry number of a chemical compound.beta12orEarlierGmelin chemical registry numberHET group nameComponent identifier code3-letter code word for a ligand (HET group) from a PDB file, for example ATP.Short ligand namebeta12orEarlierAmino acid namebeta12orEarlierString of one or more ASCII characters representing an amino acid.Nucleotide codebeta12orEarlierString of one or more ASCII characters representing a nucleotide.Polypeptide chain IDThis is typically a character (for the chain) appended to a PDB identifier, e.g. 1cukAPDB strand idPDBML:pdbx_PDB_strand_idPDB chain identifierbeta12orEarlierPolypeptide chain identifierProtein chain identifierWHATIF: chainChain identifierIdentifier of a polypeptide chain from a protein.Protein nameName of a protein.beta12orEarlierEnzyme identifierbeta12orEarlierName or other identifier of an enzyme or record from a database of enzymes.EC numberMoby:EC_Number[0-9]+\.-\.-\.-|[0-9]+\.[0-9]+\.-\.-|[0-9]+\.[0-9]+\.[0-9]+\.-|[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+ECMoby:Annotated_EC_Numberbeta12orEarlierEC codeEnzyme Commission numberAn Enzyme Commission (EC) number of an enzyme.Enzyme namebeta12orEarlierName of an enzyme.Restriction enzyme nameName of a restriction enzyme.beta12orEarlierSequence position specificationA specification (partial or complete) of one or more positions or regions of a molecular sequence or map.beta12orEarliertrue1.5Sequence feature IDA unique identifier of molecular sequence feature, for example an ID of a feature that is unique within the scope of the GFF file.beta12orEarlierSequence positionWHATIF: numberWHATIF: PDBx_atom_sitePDBML:_atom_site.idSO:0000735A position of one or more points (base or residue) in a sequence, or part of such a specification.beta12orEarlierSequence rangebeta12orEarlierSpecification of range(s) of sequence positions.Nucleic acid feature identifierName or other identifier of an nucleic acid feature.truebeta12orEarlierbeta12orEarlierProtein feature identifierbeta12orEarliertruebeta12orEarlierName or other identifier of a protein feature.Sequence feature keyThe type of a sequence feature, typically a term or accession from the Sequence Ontology, for example an EMBL or Swiss-Prot sequence feature key.A feature key indicates the biological nature of the feature or information about changes to or versions of the sequence.Sequence feature methodSequence feature typebeta12orEarlierSequence feature qualifierbeta12orEarlierTypically one of the EMBL or Swiss-Prot feature qualifiers.Feature qualifiers hold information about a feature beyond that provided by the feature key and location.Sequence feature labelSequence feature nameA feature label identifies a feature of a sequence database entry. When used with the database name and the entry's primary accession number, it is a unique identifier of that feature.A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user. Typically an EMBL or Swiss-Prot feature label.beta12orEarlierEMBOSS Uniform Feature ObjectUFObeta12orEarlierThe name of a sequence feature-containing entity adhering to the standard feature naming scheme used by all EMBOSS applications.Codon namebeta12orEarlierbeta12orEarliertrueString of one or more ASCII characters representing a codon.Gene identifierMoby:GeneAccessionListbeta12orEarlierAn identifier of a gene, such as a name/symbol or a unique identifier of a gene in a database.Gene symbolbeta12orEarlierMoby_namespace:Global_GeneSymbolMoby_namespace:Global_GeneCommonNameThe short name of a gene; a single word that does not contain white space characters. It is typically derived from the gene name.Gene ID (NCBI)Gene identifier (Entrez)NCBI gene IDhttp://www.geneontology.org/doc/GO.xrf_abbs:NCBI_GeneNCBI geneidbeta12orEarlierEntrez gene IDAn NCBI unique identifier of a gene.Gene identifier (NCBI)http://www.geneontology.org/doc/GO.xrf_abbs:LocusIDGene identifier (NCBI RefSeq)beta12orEarlierbeta12orEarliertrueAn NCBI RefSeq unique identifier of a gene.Gene identifier (NCBI UniGene)beta12orEarliertruebeta12orEarlierAn NCBI UniGene unique identifier of a gene.Gene identifier (Entrez)truebeta12orEarlier[0-9]+beta12orEarlierAn Entrez unique identifier of a gene.Gene ID (CGD)CGD IDIdentifier of a gene or feature from the CGD database.beta12orEarlierGene ID (DictyBase)beta12orEarlierIdentifier of a gene from DictyBase.Ensembl gene IDGene ID (Ensembl)beta12orEarlierUnique identifier for a gene (or other feature) from the Ensembl database.Gene ID (SGD)SGD identifierbeta12orEarlierS[0-9]+Identifier of an entry from the SGD database.Gene ID (GeneDB)beta12orEarlierGeneDB identifier[a-zA-Z_0-9\.-]*Identifier of a gene from the GeneDB database.Moby_namespace:GeneDBTIGR identifierIdentifier of an entry from the TIGR database.beta12orEarlierTAIR accession (gene)beta12orEarlierGene:[0-9]{7}Identifier of an gene from the TAIR database.Protein domain IDIdentifier of a protein structural domain.This is typically a character or string concatenated with a PDB identifier and a chain identifier.beta12orEarlierSCOP domain identifierIdentifier of a protein domain (or other node) from the SCOP database.beta12orEarlierCATH domain ID1nr3A00Identifier of a protein domain from CATH.beta12orEarlierCATH domain identifierSCOP concise classification string (sccs)beta12orEarlierA SCOP concise classification string (sccs) is a compact representation of a SCOP domain classification.An scss includes the class (alphabetical), fold, superfamily and family (all numerical) to which a given domain belongs.SCOP sunidA sunid uniquely identifies an entry in the SCOP hierarchy, including leaves (the SCOP domains) and higher level nodes including entries corresponding to the protein level.33229sunidUnique identifier (number) of an entry in the SCOP hierarchy, for example 33229.SCOP unique identifierbeta12orEarlierCATH node IDCATH node identifier3.30.1190.10.1.1.1.1.1A code number identifying a node from the CATH database.CATH codebeta12orEarlierKingdom namebeta12orEarlierThe name of a biological kingdom (Bacteria, Archaea, or Eukaryotes).Species nameOrganism speciesbeta12orEarlierThe name of a species (typically a taxonomic group) of organism.Strain namebeta12orEarlierThe name of a strain of an organism variant, typically a plant, virus or bacterium.URIA string of characters that name or otherwise identify a resource on the Internet.beta12orEarlierURIsDatabase IDbeta12orEarlierDatabase identifierAn identifier of a biological or bioinformatics database.Directory nameThe name of a directory.beta12orEarlierFile namebeta12orEarlierThe name (or part of a name) of a file (of any type).Ontology namebeta12orEarlierName of an ontology of biological or bioinformatics concepts and relations.URLbeta12orEarlierA Uniform Resource Locator (URL).Moby:LinkMoby:URLURNA Uniform Resource Name (URN).beta12orEarlierLSIDA Life Science Identifier (LSID) - a unique identifier of some data.LSIDs provide a standard way to locate and describe data. An LSID is represented as a Uniform Resource Name (URN) with the following format: URN:LSID:<Authority>:<Namespace>:<ObjectID>[:<Version>]Life Science Identifierbeta12orEarlierDatabase nameThe name of a biological or bioinformatics database.beta12orEarlierSequence database nametruebeta12orEarlierThe name of a molecular sequence database.beta13Enumerated file namebeta12orEarlierThe name of a file (of any type) with restricted possible values.File name extensionThe extension of a file name.beta12orEarlierA file extension is the characters appearing after the final '.' in the file name.File base nameA file base name is the file name stripped of its directory specification and extension.beta12orEarlierThe base name of a file.QSAR descriptor nameName of a QSAR descriptor.beta12orEarlierDatabase entry identifierbeta12orEarlierThis concept is required for completeness. It should never have child concepts.beta12orEarliertrueAn identifier of an entry from a database where the same type of identifier is used for objects (data) of different semantic type.Sequence identifierbeta12orEarlierAn identifier of molecular sequence(s) or entries from a molecular sequence database.Sequence set IDAn identifier of a set of molecular sequence(s).beta12orEarlierSequence signature identifiertruebeta12orEarlierbeta12orEarlierIdentifier of a sequence signature (motif or profile) for example from a database of sequence patterns.Sequence alignment IDIdentifier of a molecular sequence alignment, for example a record from an alignment database.beta12orEarlierPhylogenetic distance matrix identifiertrueIdentifier of a phylogenetic distance matrix.beta12orEarlierbeta12orEarlierPhylogenetic tree IDbeta12orEarlierIdentifier of a phylogenetic tree for example from a phylogenetic tree database.Comparison matrix identifierAn identifier of a comparison matrix.beta12orEarlierSubstitution matrix identifierStructure IDA unique and persistent identifier of a molecular tertiary structure, typically an entry from a structure database.beta12orEarlierStructural (3D) profile IDStructural profile identifierbeta12orEarlierIdentifier or name of a structural (3D) profile or template (representing a structure or structure alignment).Structure alignment IDbeta12orEarlierIdentifier of an entry from a database of tertiary structure alignments.Amino acid index IDbeta12orEarlierIdentifier of an index of amino acid physicochemical and biochemical property data.Protein interaction IDIdentifier of a report of protein interactions from a protein interaction database (typically).beta12orEarlierMolecular interaction IDProtein family identifierIdentifier of a protein family.Protein secondary database record identifierbeta12orEarlierCodon usage table namebeta12orEarlierUnique name of a codon usage table.Transcription factor identifierIdentifier of a transcription factor (or a TF binding site).beta12orEarlierExperiment annotation IDIdentifier of an entry from a database of microarray data.beta12orEarlierElectron microscopy model IDbeta12orEarlierIdentifier of an entry from a database of electron microscopy data.Gene expression report IDbeta12orEarlierAccession of a report of gene expression (e.g. a gene expression profile) from a database.Gene expression profile identifierGenotype and phenotype annotation IDbeta12orEarlierIdentifier of an entry from a database of genotypes and phenotypes.Pathway or network identifierIdentifier of an entry from a database of biological pathways or networks.beta12orEarlierWorkflow IDIdentifier of a biological or biomedical workflow, typically from a database of workflows.beta12orEarlierData resource definition IDbeta12orEarlierIdentifier of a data type definition from some provider.Data resource definition identifierBiological model IDBiological model identifierIdentifier of a mathematical model, typically an entry from a database.beta12orEarlierCompound identifierIdentifier of an entry from a database of chemicals.beta12orEarlierSmall molecule identifierChemical compound identifierOntology concept IDA unique (typically numerical) identifier of a concept in an ontology of biological or bioinformatics concepts and relations.beta12orEarlierArticle IDbeta12orEarlierUnique identifier of a scientific article.Article identifierFlyBase IDFB[a-zA-Z_0-9]{2}[0-9]{7}beta12orEarlierIdentifier of an object from the FlyBase database.WormBase namebeta12orEarlierName of an object from the WormBase database, usually a human-readable name.WormBase classbeta12orEarlierClass of an object from the WormBase database.A WormBase class describes the type of object such as 'sequence' or 'protein'.Sequence accessionSequence accession numberA persistent, unique identifier of a molecular sequence database entry.beta12orEarlierSequence typeA label (text token) describing a type of molecular sequence.1.5truebeta12orEarlierSequence type might reflect the molecule (protein, nucleic acid etc) or the sequence itself (gapped, ambiguous etc).EMBOSS Uniform Sequence Addressbeta12orEarlierEMBOSS USAThe name of a sequence-based entity adhering to the standard sequence naming scheme used by all EMBOSS applications.Sequence accession (protein)Protein sequence accession numberAccession number of a protein sequence database entry.beta12orEarlierSequence accession (nucleic acid)Accession number of a nucleotide sequence database entry.beta12orEarlierNucleotide sequence accession numberRefSeq accessionAccession number of a RefSeq database entry.RefSeq IDbeta12orEarlier(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|YP|ZP)_[0-9]+UniProt accession (extended)[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]|[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9].[0-9]+|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9].[0-9]+|[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]-[0-9]+|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]-[0-9]+Q7M1G0|P43353-2|P01012.107beta12orEarliertrue1.0Accession number of a UniProt (protein sequence) database entry. May contain version or isoform number.PIR identifierPIR accession numberbeta12orEarlierAn identifier of PIR sequence database entry.PIR IDTREMBL accessionbeta12orEarliertrue1.2Identifier of a TREMBL sequence database entry.Gramene primary identifierPrimary identifier of a Gramene database entry.Gramene primary IDbeta12orEarlierEMBL/GenBank/DDBJ IDbeta12orEarlierIdentifier of a (nucleic acid) entry from the EMBL/GenBank/DDBJ databases.Sequence cluster ID (UniGene)UniGene cluster IDUniGene cluster idUniGene identifierbeta12orEarlierA unique identifier of an entry (gene cluster) from the NCBI UniGene database.UniGene IDdbEST accessionIdentifier of a dbEST database entry.beta12orEarlierdbEST IDdbSNP IDdbSNP identifierIdentifier of a dbSNP database entry.beta12orEarlierEMBOSS sequence typebeta12orEarlierSee the EMBOSS documentation (http://emboss.sourceforge.net/) for a definition of what this includes.The EMBOSS type of a molecular sequence.truebeta12orEarlierEMBOSS listfile1.5beta12orEarliertrueList of EMBOSS Uniform Sequence Addresses (EMBOSS listfile).Sequence cluster IDbeta12orEarlierAn identifier of a cluster of molecular sequence(s).Sequence cluster ID (COG)COG IDUnique identifier of an entry from the COG database.beta12orEarlierSequence motif identifierbeta12orEarlierIdentifier of a sequence motif, for example an entry from a motif database.Sequence profile IDA sequence profile typically represents a sequence alignment.Identifier of a sequence profile.beta12orEarlierELM IDbeta12orEarlierIdentifier of an entry from the ELMdb database of protein functional sites.Prosite accession numberPS[0-9]{5}beta12orEarlierAccession number of an entry from the Prosite database.Prosite IDHMMER hidden Markov model IDUnique identifier or name of a HMMER hidden Markov model.beta12orEarlierJASPAR profile IDUnique identifier or name of a profile from the JASPAR database.beta12orEarlierSequence alignment type1.5A label (text token) describing the type of a sequence alignment.truebeta12orEarlierPossible values include for example the EMBOSS alignment types, BLAST alignment types and so on.BLAST sequence alignment typetruebeta12orEarlierbeta12orEarlierThe type of a BLAST sequence alignment.Phylogenetic tree typeA label (text token) describing the type of a phylogenetic tree.nj|upgmpFor example 'nj', 'upgmp' etc.1.5truebeta12orEarlierTreeBASE study accession numberAccession number of an entry from the TreeBASE database.beta12orEarlierTreeFam accession numberbeta12orEarlierAccession number of an entry from the TreeFam database.Comparison matrix typeFor example 'blosum', 'pam', 'gonnet', 'id' etc. Comparison matrix type may be required where a series of matrices of a certain type are used.blosum|pam|gonnet|id1.5A label (text token) describing the type of a comparison matrix.beta12orEarliertrueComparison matrix namebeta12orEarlierUnique name or identifier of a comparison matrix.Substitution matrix nameSee for example http://www.ebi.ac.uk/Tools/webservices/help/matrix.PDB IDAn identifier of an entry from the PDB database.PDBIDPDB identifierbeta12orEarlier[a-zA-Z_0-9]{4}AAindex IDbeta12orEarlierIdentifier of an entry from the AAindex database.BIND accession numberAccession number of an entry from the BIND database.beta12orEarlierIntAct accession numberbeta12orEarlierAccession number of an entry from the IntAct database.EBI\-[0-9]+Protein family nameName of a protein family.beta12orEarlierInterPro entry namebeta12orEarlierName of an InterPro entry, usually indicating the type of protein matches for that entry.InterPro accessionEvery InterPro entry has a unique accession number to provide a persistent citation of database records.beta12orEarlierPrimary accession number of an InterPro entry.IPR[0-9]{6}IPR015590InterPro primary accessionInterPro primary accession numberInterPro secondary accessionSecondary accession number of an InterPro entry.InterPro secondary accession numberbeta12orEarlierGene3D IDbeta12orEarlierUnique identifier of an entry from the Gene3D database.PIRSF IDUnique identifier of an entry from the PIRSF database.PIRSF[0-9]{6}beta12orEarlierPRINTS codebeta12orEarlierPR[0-9]{5}The unique identifier of an entry in the PRINTS database.Pfam accession numberPF[0-9]{5}Accession number of a Pfam entry.beta12orEarlierSMART accession numberAccession number of an entry from the SMART database.beta12orEarlierSM[0-9]{5}Superfamily hidden Markov model numberUnique identifier (number) of a hidden Markov model from the Superfamily database.beta12orEarlierTIGRFam IDAccession number of an entry (family) from the TIGRFam database.beta12orEarlierTIGRFam accession numberProDom accession numberA ProDom domain family accession number.beta12orEarlierProDom is a protein domain family database.PD[0-9]+TRANSFAC accession numberbeta12orEarlierIdentifier of an entry from the TRANSFAC database.ArrayExpress accession number[AEP]-[a-zA-Z_0-9]{4}-[0-9]+ArrayExpress experiment IDbeta12orEarlierAccession number of an entry from the ArrayExpress database.PRIDE experiment accession number[0-9]+beta12orEarlierPRIDE experiment accession number.EMDB IDIdentifier of an entry from the EMDB electron microscopy database.beta12orEarlierGEO accession numbero^GDS[0-9]+Accession number of an entry from the GEO database.beta12orEarlierGermOnline IDbeta12orEarlierIdentifier of an entry from the GermOnline database.EMAGE IDIdentifier of an entry from the EMAGE database.beta12orEarlierDisease IDbeta12orEarlierAccession number of an entry from a database of disease.HGVbase IDIdentifier of an entry from the HGVbase database.beta12orEarlierHIVDB identifiertruebeta12orEarlierIdentifier of an entry from the HIVDB database.beta12orEarlierOMIM ID[*#+%^]?[0-9]{6}beta12orEarlierIdentifier of an entry from the OMIM database.KEGG object identifierbeta12orEarlierUnique identifier of an object from one of the KEGG databases (excluding the GENES division).Pathway ID (reactome)Identifier of an entry from the Reactome database.beta12orEarlierReactome IDREACT_[0-9]+(\.[0-9]+)?Pathway ID (aMAZE)aMAZE IDbeta12orEarliertruebeta12orEarlierIdentifier of an entry from the aMAZE database.Pathway ID (BioCyc)beta12orEarlierBioCyc pathway IDIdentifier of an pathway from the BioCyc biological pathways database.Pathway ID (INOH)INOH identifierIdentifier of an entry from the INOH database.beta12orEarlierPathway ID (PATIKA)Identifier of an entry from the PATIKA database.beta12orEarlierPATIKA IDPathway ID (CPDB)Identifier of an entry from the CPDB (ConsensusPathDB) biological pathways database, which is an identifier from an external database integrated into CPDB.beta12orEarlierThis concept refers to identifiers used by the databases collated in CPDB; CPDB identifiers are not independently defined.CPDB IDPathway ID (Panther)beta12orEarlierIdentifier of a biological pathway from the Panther Pathways database.PTHR[0-9]{5}Panther Pathways IDMIRIAM identifierMIR:[0-9]{8}This is the identifier used internally by MIRIAM for a data type.Unique identifier of a MIRIAM data resource.MIR:00100005beta12orEarlierMIRIAM data type namebeta12orEarlierThe name of a data type from the MIRIAM database.MIRIAM URIA MIRIAM URI consists of the URI of the MIRIAM data type (PubMed, UniProt etc) followed by the identifier of an element of that data type, for example PMID for a publication or an accession number for a GO term.urn:miriam:pubmed:16333295|urn:miriam:obo.go:GO%3A0045202beta12orEarlieridentifiers.org synonymThe URI (URL or URN) of a data entity from the MIRIAM database.MIRIAM data type primary namebeta12orEarlierThe primary name of a data type from the MIRIAM database.UniProt|Enzyme NomenclatureThe primary name of a MIRIAM data type is taken from a controlled vocabulary.UniProt|Enzyme NomenclatureA protein entity has the MIRIAM data type 'UniProt', and an enzyme has the MIRIAM data type 'Enzyme Nomenclature'.MIRIAM data type synonymous nameA synonymous name of a data type from the MIRIAM database.A synonymous name for a MIRIAM data type taken from a controlled vocabulary.beta12orEarlierTaverna workflow IDUnique identifier of a Taverna workflow.beta12orEarlierBiological model nameName of a biological (mathematical) model.beta12orEarlierBioModel ID(BIOMD|MODEL)[0-9]{10}Unique identifier of an entry from the BioModel database.beta12orEarlierPubChem CIDPubChem compound accession identifierChemical structure specified in PubChem Compound Identification (CID), a non-zero integer identifier for a unique chemical structure.[0-9]+beta12orEarlierChemSpider IDIdentifier of an entry from the ChemSpider database.[0-9]+beta12orEarlierChEBI IDbeta12orEarlierIdentifier of an entry from the ChEBI database.ChEBI IDsChEBI identifierCHEBI:[0-9]+BioPax concept IDAn identifier of a concept from the BioPax ontology.beta12orEarlierGO concept IDbeta12orEarlierGO concept identifierAn identifier of a concept from The Gene Ontology.[0-9]{7}|GO:[0-9]{7}MeSH concept IDAn identifier of a concept from the MeSH vocabulary.beta12orEarlierHGNC concept IDAn identifier of a concept from the HGNC controlled vocabulary.beta12orEarlierNCBI taxonomy ID[1-9][0-9]{0,8}9662|3483|182682NCBI taxonomy identifierNCBI tax IDbeta12orEarlierA stable unique identifier for each taxon (for a species, a family, an order, or any other group in the NCBI taxonomy database.Plant Ontology concept IDbeta12orEarlierAn identifier of a concept from the Plant Ontology (PO).UMLS concept IDbeta12orEarlierAn identifier of a concept from the UMLS vocabulary.FMA concept IDbeta12orEarlierFMA:[0-9]+Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented.An identifier of a concept from Foundational Model of Anatomy.EMAP concept IDbeta12orEarlierAn identifier of a concept from the EMAP mouse ontology.ChEBI concept IDAn identifier of a concept from the ChEBI ontology.beta12orEarlierMGED concept IDbeta12orEarlierAn identifier of a concept from the MGED ontology.myGrid concept IDThe ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services.An identifier of a concept from the myGrid ontology.beta12orEarlierPubMed IDPMIDPubMed unique identifier of an article.4963447beta12orEarlier[1-9][0-9]{0,8}DOIDigital Object Identifier (DOI) of a published article.Digital Object Identifierbeta12orEarlier(doi\:)?[0-9]{2}\.[0-9]{4}/.*Medline UIThe use of Medline UI has been replaced by the PubMed unique identifier.beta12orEarlierMedline unique identifierMedline UI (unique identifier) of an article.Tool nameThe name of a computer package, application, method or function.beta12orEarlierTool name (signature)beta12orEarlierSignature methods from http://www.ebi.ac.uk/Tools/InterProScan/help.html#results include BlastProDom, FPrintScan, HMMPIR, HMMPfam, HMMSmart, HMMTigr, ProfileScan, ScanRegExp, SuperFamily and HAMAP.The unique name of a signature (sequence classifier) method.Tool name (BLAST)BLAST namebeta12orEarlierThe name of a BLAST tool.This include 'blastn', 'blastp', 'blastx', 'tblastn' and 'tblastx'.Tool name (FASTA)The name of a FASTA tool.This includes 'fasta3', 'fastx3', 'fasty3', 'fastf3', 'fasts3' and 'ssearch'.beta12orEarlierTool name (EMBOSS)beta12orEarlierThe name of an EMBOSS application.Tool name (EMBASSY package)The name of an EMBASSY package.beta12orEarlierQSAR descriptor (constitutional)QSAR constitutional descriptorbeta12orEarlierA QSAR constitutional descriptor.QSAR descriptor (electronic)A QSAR electronic descriptor.QSAR electronic descriptorbeta12orEarlierQSAR descriptor (geometrical)A QSAR geometrical descriptor.QSAR geometrical descriptorbeta12orEarlierQSAR descriptor (topological)beta12orEarlierA QSAR topological descriptor.QSAR topological descriptorQSAR descriptor (molecular)beta12orEarlierA QSAR molecular descriptor.QSAR molecular descriptorSequence set (protein)Any collection of multiple protein sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries.beta12orEarlierSequence set (nucleic acid)beta12orEarlierAny collection of multiple nucleotide sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries.Sequence clusterThe cluster might include sequences identifiers, short descriptions, alignment and summary information.beta12orEarlierA set of sequences that have been clustered or otherwise classified as belonging to a group including (typically) sequence cluster information.Psiblast checkpoint filetruebeta12orEarlierA file of intermediate results from a PSIBLAST search that is used for priming the search in the next PSIBLAST iteration.A Psiblast checkpoint file uses ASN.1 Binary Format and usually has the extension '.asn'.beta12orEarlierHMMER synthetic sequences setbeta12orEarlierSequences generated by HMMER package in FASTA-style format.truebeta12orEarlierProteolytic digestbeta12orEarlierA protein sequence cleaved into peptide fragments (by enzymatic or chemical cleavage) with fragment masses.Restriction digestSO:0000412Restriction digest fragments from digesting a nucleotide sequence with restriction sites using a restriction endonuclease.beta12orEarlierPCR primersbeta12orEarlierOligonucleotide primer(s) for PCR and DNA amplification, for example a minimal primer set.vectorstrip cloning vector definition filebeta12orEarlierFile of sequence vectors used by EMBOSS vectorstrip application, or any file in same format.truebeta12orEarlierPrimer3 internal oligo mishybridizing librarytruebeta12orEarlierbeta12orEarlierA library of nucleotide sequences to avoid during hybridisation events. Hybridisation of the internal oligo to sequences in this library is avoided, rather than priming from them. The file is in a restricted FASTA format.Primer3 mispriming library filebeta12orEarlierA nucleotide sequence library of sequences to avoid during amplification (for example repetitive sequences, or possibly the sequences of genes in a gene family that should not be amplified. The file must is in a restricted FASTA format.beta12orEarliertrueprimersearch primer pairs sequence recordbeta12orEarlierFile of one or more pairs of primer sequences, as used by EMBOSS primersearch application.beta12orEarliertrueSequence cluster (protein)beta12orEarlierA cluster of protein sequences.Protein sequence clusterThe sequences are typically related, for example a family of sequences.Sequence cluster (nucleic acid)Nucleotide sequence clusterThe sequences are typically related, for example a family of sequences.beta12orEarlierA cluster of nucleotide sequences.Sequence lengthThe size (length) of a sequence, subsequence or region in a sequence, or range(s) of lengths.beta12orEarlierWord sizeSize of a sequence word.Word size is used for example in word-based sequence database search methods.truebeta12orEarlier1.5Window sizebeta12orEarliertrue1.5A window is a region of fixed size but not fixed position over a molecular sequence. It is typically moved (computationally) over a sequence during scoring.Size of a sequence window.Sequence length range1.5truebeta12orEarlierSpecification of range(s) of length of sequences.Sequence information reporttruebeta12orEarlierbeta12orEarlierReport on basic information about a molecular sequence such as name, accession number, type (nucleic or protein), length, description etc.Sequence propertySequence properties reportAn informative report about non-positional sequence features, typically a report on general molecular sequence properties derived from sequence analysis.beta12orEarlierSequence featureshttp://purl.bioontology.org/ontology/MSH/D058977This includes annotation of positional sequence features, organised into a standard feature table, or any other report of sequence features. General feature reports are a source of sequence feature table information although internal conversion would be required.Annotation of positional features of molecular sequence(s), i.e. that can be mapped to position(s) in the sequence.FeaturesSO:0000110Sequence features reportFeature recordbeta12orEarlierGeneral sequence featuresSequence features (comparative)beta12orEarliertrueThis is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.beta13Comparative data on sequence features such as statistics, intersections (and data on intersections), differences etc.Sequence property (protein)beta12orEarlierbeta12orEarliertrueA report of general sequence properties derived from protein sequence data.Sequence property (nucleic acid)truebeta12orEarlierA report of general sequence properties derived from nucleotide sequence data.beta12orEarlierSequence complexity reportSequence property (complexity)A report on sequence complexity, for example low-complexity or repeat regions in sequences.beta12orEarlierSequence ambiguity reportbeta12orEarlierA report on ambiguity in molecular sequence(s).Sequence property (ambiguity)Sequence composition reportA report (typically a table) on character or word composition / frequency of a molecular sequence(s).beta12orEarlierSequence property (composition)Peptide molecular weight hitsbeta12orEarlierA report on peptide fragments of certain molecular weight(s) in one or more protein sequences.Base position variability plotA plot of third base position variability in a nucleotide sequence.beta12orEarlierSequence composition tablebeta12orEarliertruebeta12orEarlierA table of character or word composition / frequency of a molecular sequence.Base frequencies tableA table of base frequencies of a nucleotide sequence.beta12orEarlierBase word frequencies tablebeta12orEarlierA table of word composition of a nucleotide sequence.Amino acid frequencies tablebeta12orEarlierSequence composition (amino acid frequencies)A table of amino acid frequencies of a protein sequence.Amino acid word frequencies tableA table of amino acid word composition of a protein sequence.beta12orEarlierSequence composition (amino acid words)DAS sequence feature annotationtruebeta12orEarlierAnnotation of a molecular sequence in DAS format.beta12orEarlierFeature tableAnnotation of positional sequence features, organised into a standard feature table.beta12orEarlierSequence feature tableMapA map of (typically one) DNA sequence annotated with positional or non-positional features.beta12orEarlierDNA mapNucleic acid featuresGenomic featuresGenome featuresFeature table (nucleic acid)This includes nucleotide sequence feature annotation in any known sequence feature table format and any other report of nucleic acid features.An informative report on intrinsic positional features of a nucleotide sequence.Nucleic acid feature tablebeta12orEarlierProtein featuresAn informative report on intrinsic positional features of a protein sequence.Feature table (protein)beta12orEarlierProtein feature tableThis includes protein sequence feature annotation in any known sequence feature table format and any other report of protein features.Genetic mapbeta12orEarlierA genetic (linkage) map indicates the proximity of two genes on a chromosome, whether two genes are linked and the frequency they are transmitted together to an offspring. They are limited to genetic markers of traits observable only in whole organisms.Moby:GeneticMapLinkage mapA map showing the relative positions of genetic markers in a nucleic acid sequence, based on estimation of non-physical distance such as recombination frequencies.Sequence mapbeta12orEarlierA sequence map typically includes annotation on significant subsequences such as contigs, haplotypes and genes. The contigs shown will (typically) be a set of small overlapping clones representing a complete chromosomal segment.A map of genetic markers in a contiguous, assembled genomic sequence, with the sizes and separation of markers measured in base pairs.Physical mapA map of DNA (linear or circular) annotated with physical features or landmarks such as restriction sites, cloned DNA fragments, genes or genetic markers, along with the physical distances between them.Distance in a physical map is measured in base pairs. A physical map might be ordered relative to a reference map (typically a genetic map) in the process of genome sequencing.beta12orEarlierSequence signature mapImage of a sequence with matches to signatures, motifs or profiles.beta12orEarliertruebeta12orEarlierCytogenetic mapThis is the lowest-resolution physical map and can provide only rough estimates of physical (base pair) distances. Like a genetic map, they are limited to genetic markers of traits observable only in whole organisms.A map showing banding patterns derived from direct observation of a stained chromosome.beta12orEarlierCytologic mapCytogenic mapChromosome mapDNA transduction mapA gene map showing distances between loci based on relative cotransduction frequencies.beta12orEarlierGene mapbeta12orEarlierSequence map of a single gene annotated with genetic features such as introns, exons, untranslated regions, polyA signals, promoters, enhancers and (possibly) mutations defining alleles of a gene.Plasmid mapSequence map of a plasmid (circular DNA).beta12orEarlierGenome mapbeta12orEarlierSequence map of a whole genome.Restriction mapImage of the restriction enzyme cleavage sites (restriction sites) in a nucleic acid sequence.beta12orEarlierInterPro compact match imageThe sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Each protein is represented as a scaled horizontal line with colored bars indicating the position of the matches.truebeta12orEarlierbeta12orEarlierImage showing matches between protein sequence(s) and InterPro Entries.InterPro detailed match imageImage showing detailed information on matches between protein sequence(s) and InterPro Entries.beta12orEarlierbeta12orEarlierThe sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself.trueInterPro architecture imagebeta12orEarlierThe sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Domain architecture is shown as a series of non-overlapping domains in the protein.truebeta12orEarlierImage showing the architecture of InterPro domains in a protein sequence.SMART protein schematicSMART protein schematic in PNG format.beta12orEarlierbeta12orEarliertrueGlobPlot domain imagebeta12orEarliertruebeta12orEarlierImages based on GlobPlot prediction of intrinsic disordered regions and globular domains in protein sequences.Sequence motif matchestruebeta12orEarlierReport on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more sequences.1.8Sequence features (repeats)The report might include derived data map such as classification, annotation, organisation, periodicity etc.1.5Location of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences.beta12orEarliertrueGene and transcript structure (report)truebeta12orEarlier1.5A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc.Mobile genetic elements1.8beta12orEarliertrueregions of a nucleic acid sequence containing mobile genetic elements.Nucleic acid features report (PolyA signal or site)regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript.truebeta12orEarlier1.8Nucleic acid features (quadruplexes)A report on quadruplex-forming motifs in a nucleotide sequence.truebeta12orEarlier1.5Nucleic acid features report (CpG island and isochore)1.8truebeta12orEarlierCpG rich regions (isochores) in a nucleotide sequence.Nucleic acid features report (restriction sites)restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence.1.8beta12orEarliertrueNucleosome exclusion sequences1.8beta12orEarliertrueReport on nucleosome formation potential or exclusion sequence(s).Nucleic acid features report (splice sites)truebeta12orEarliersplice sites in a nucleotide sequence or alternative RNA splicing events.1.8Nucleic acid features report (matrix/scaffold attachment sites)matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence.truebeta12orEarlier1.8Gene features (exonic splicing enhancer)beta13truebeta12orEarlierA report on exonic splicing enhancers (ESE) in an exon.Nucleic acid features (microRNA)1.5truebeta12orEarlierA report on microRNA sequence (miRNA) or precursor, microRNA targets, miRNA binding sites in an RNA sequence etc.Gene features report (operon)beta12orEarliertrue1.8operons (operators, promoters and genes) from a bacterial genome.Nucleic acid features report (promoters)whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence.truebeta12orEarlier1.8Coding regiontruebeta12orEarlier1.8protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames.Gene features (SECIS element)A report on selenocysteine insertion sequence (SECIS) element in a DNA sequence.beta13beta12orEarliertrueTranscription factor binding sites1.8truetranscription factor binding sites (TFBS) in a DNA sequence.beta12orEarlierProtein features (sites)beta12orEarliertrueA report on predicted or known key residue positions (sites) in a protein sequence, such as binding or functional sites.beta12orEarlierUse this concept for collections of specific sites which are not necessarily contiguous, rather than contiguous stretches of amino acids.Protein features report (signal peptides)1.8truebeta12orEarliersignal peptides or signal peptide cleavage sites in protein sequences.Protein features report (cleavage sites)cleavage sites (for a proteolytic enzyme or agent) in a protein sequence.truebeta12orEarlier1.8Protein features (post-translation modifications)1.8post-translation modifications in a protein sequence, typically describing the specific sites involved.beta12orEarliertrueProtein features report (active sites)truebeta12orEarliercatalytic residues (active site) of an enzyme.1.8Protein features report (binding sites)1.8truebeta12orEarlierligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids.Protein features (epitopes)beta12orEarliertrueA report on antigenic determinant sites (epitopes) in proteins, from sequence and / or structural data.beta13Epitope mapping is commonly done during vaccine design.Protein features report (nucleic acid binding sites)1.8truebeta12orEarlierRNA and DNA-binding proteins and binding sites in protein sequences.MHC Class I epitopes reportA report on epitopes that bind to MHC class I molecules.beta12orEarliertruebeta12orEarlierMHC Class II epitopes reportbeta12orEarliertrueA report on predicted epitopes that bind to MHC class II molecules.beta12orEarlierProtein features (PEST sites)truebeta12orEarlierbeta13'PEST' motifs target proteins for proteolytic degradation and reduce the half-lives of proteins dramatically.A report or plot of PEST sites in a protein sequence.Sequence database hits scores listtruebeta12orEarlierbeta12orEarlierScores from a sequence database search (for example a BLAST search).Sequence database hits alignments listAlignments from a sequence database search (for example a BLAST search).beta12orEarliertruebeta12orEarlierSequence database hits evaluation datatruebeta12orEarlierA report on the evaluation of the significance of sequence similarity scores from a sequence database search (for example a BLAST search).beta12orEarlierMEME motif alphabetAlphabet for the motifs (patterns) that MEME will search for.beta12orEarliertruebeta12orEarlierMEME background frequencies filebeta12orEarlierbeta12orEarliertrueMEME background frequencies file.MEME motifs directive fileFile of directives for ordering and spacing of MEME motifs.beta12orEarlierbeta12orEarliertrueDirichlet distributionbeta12orEarlierDirichlet distribution used by hidden Markov model analysis programs.HMM emission and transition counts1.4Emission and transition counts of a hidden Markov model, generated once HMM has been determined, for example after residues/gaps have been assigned to match, delete and insert states.beta12orEarliertrueRegular expressionRegular expression pattern.beta12orEarlierSequence motifbeta12orEarlierAny specific or conserved pattern (typically expressed as a regular expression) in a molecular sequence.Sequence profilebeta12orEarlierhttp://semanticscience.org/resource/SIO_010531Some type of statistical model representing a (typically multiple) sequence alignment.Protein signatureAn informative report about a specific or conserved protein sequence pattern.Protein domain signatureProtein site signatureProtein region signatureInterPro entryProtein family signatureProtein repeat signaturebeta12orEarlierProsite nucleotide patternbeta12orEarliertrueA nucleotide regular expression pattern from the Prosite database.beta12orEarlierProsite protein patternA protein regular expression pattern from the Prosite database.truebeta12orEarlierbeta12orEarlierPosition frequency matrixPFMA profile (typically representing a sequence alignment) that is a simple matrix of nucleotide (or amino acid) counts per position.beta12orEarlierPosition weight matrixbeta12orEarlierPWMContributions of individual sequences to the matrix might be uneven (weighted).A profile (typically representing a sequence alignment) that is weighted matrix of nucleotide (or amino acid) counts per position.Information content matrixA profile (typically representing a sequence alignment) derived from a matrix of nucleotide (or amino acid) counts per position that reflects information content at each position.ICMbeta12orEarlierHidden Markov modelbeta12orEarlierA statistical Markov model of a system which is assumed to be a Markov process with unobserved (hidden) states. For example, a hidden Markov model representation of a set or alignment of sequences.HMMFingerprintbeta12orEarlierOne or more fingerprints (sequence classifiers) as used in the PRINTS database.Domainatrix signatureA protein signature of the type used in the EMBASSY Signature package.beta12orEarliertruebeta12orEarlierHMMER NULL hidden Markov modelbeta12orEarliertruebeta12orEarlierNULL hidden Markov model representation used by the HMMER package.Protein family signature1.5truebeta12orEarlierProtein family signatures cover all domains in the matching proteins and span >80% of the protein length and with no adjacent protein domain signatures or protein region signatures.A protein family signature (sequence classifier) from the InterPro database.Protein domain signaturetruebeta12orEarlierA protein domain signature (sequence classifier) from the InterPro database.Protein domain signatures identify structural or functional domains or other units with defined boundaries.1.5Protein region signature1.5A protein region signature defines a region which cannot be described as a protein family or domain signature.truebeta12orEarlierA protein region signature (sequence classifier) from the InterPro database.Protein repeat signatureA protein repeat signature is a repeated protein motif, that is not in single copy expected to independently fold into a globular domain.beta12orEarliertrue1.5A protein repeat signature (sequence classifier) from the InterPro database.Protein site signatureA protein site signature is a classifier for a specific site in a protein.beta12orEarliertrue1.5A protein site signature (sequence classifier) from the InterPro database.Protein conserved site signaturebeta12orEarliertrueA protein conserved site signature (sequence classifier) from the InterPro database.A protein conserved site signature is any short sequence pattern that may contain one or more unique residues and is cannot be described as a active site, binding site or post-translational modification.1.4Protein active site signatureA protein active site signature (sequence classifier) from the InterPro database.beta12orEarlier1.4trueA protein active site signature corresponds to an enzyme catalytic pocket. An active site typically includes non-contiguous residues, therefore multiple signatures may be required to describe an active site. ; residues involved in enzymatic reactions for which mutational data is typically available.Protein binding site signatureA protein binding site signature corresponds to a site that reversibly binds chemical compounds, which are not themselves substrates of the enzymatic reaction. This includes enzyme cofactors and residues involved in electron transport or protein structure modification.1.4truebeta12orEarlierA protein binding site signature (sequence classifier) from the InterPro database.Protein post-translational modification signaturebeta12orEarliertrueA protein post-translational modification signature corresponds to sites that undergo modification of the primary structure, typically to activate or de-activate a function. For example, methylation, sumoylation, glycosylation etc. The modification might be permanent or reversible.1.4A protein post-translational modification signature (sequence classifier) from the InterPro database.Sequence alignment (pair)http://semanticscience.org/resource/SIO_010068Alignment of exactly two molecular sequences.beta12orEarlierSequence alignment (multiple)truebeta12orEarlierbeta12orEarlierAlignment of more than two molecular sequences.Sequence alignment (nucleic acid)Alignment of multiple nucleotide sequences.beta12orEarlierSequence alignment (protein)beta12orEarlierAlignment of multiple protein sequences.Sequence alignment (hybrid)Alignment of multiple molecular sequences of different types.Hybrid sequence alignments include for example genomic DNA to EST, cDNA or mRNA.beta12orEarlierSequence alignment (nucleic acid pair)truebeta12orEarlier1.12Alignment of exactly two nucleotide sequences.Sequence alignment (protein pair)truebeta12orEarlier1.12Alignment of exactly two protein sequences.Hybrid sequence alignment (pair)beta12orEarlierAlignment of exactly two molecular sequences of different types.beta12orEarliertrueMultiple nucleotide sequence alignmentbeta12orEarliertruebeta12orEarlierAlignment of more than two nucleotide sequences.Multiple protein sequence alignmentbeta12orEarlierAlignment of more than two protein sequences.beta12orEarliertrueAlignment score or penaltyA simple floating point number defining the penalty for opening or extending a gap in an alignment.beta12orEarlierScore end gaps controlWhether end gaps are scored or not.truebeta12orEarlierbeta12orEarlierAligned sequence orderbeta12orEarlierControls the order of sequences in an output sequence alignment.beta12orEarliertrueGap opening penaltybeta12orEarlierA penalty for opening a gap in an alignment.Gap extension penaltybeta12orEarlierA penalty for extending a gap in an alignment.Gap separation penaltyA penalty for gaps that are close together in an alignment.beta12orEarlierTerminal gap penaltybeta12orEarliertruebeta12orEarlierA penalty for gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences.Match reward scoreThe score for a 'match' used in various sequence database search applications with simple scoring schemes.beta12orEarlierMismatch penalty scorebeta12orEarlierThe score (penalty) for a 'mismatch' used in various alignment and sequence database search applications with simple scoring schemes.Drop off scoreThis is the threshold drop in score at which extension of word alignment is halted.beta12orEarlierGap opening penalty (integer)beta12orEarliertruebeta12orEarlierA simple floating point number defining the penalty for opening a gap in an alignment.Gap opening penalty (float)A simple floating point number defining the penalty for opening a gap in an alignment.truebeta12orEarlierbeta12orEarlierGap extension penalty (integer)A simple floating point number defining the penalty for extending a gap in an alignment.beta12orEarliertruebeta12orEarlierGap extension penalty (float)beta12orEarliertruebeta12orEarlierA simple floating point number defining the penalty for extending a gap in an alignment.Gap separation penalty (integer)A simple floating point number defining the penalty for gaps that are close together in an alignment.beta12orEarlierbeta12orEarliertrueGap separation penalty (float)beta12orEarliertruebeta12orEarlierA simple floating point number defining the penalty for gaps that are close together in an alignment.Terminal gap opening penaltyA number defining the penalty for opening gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences.beta12orEarlierTerminal gap extension penaltyA number defining the penalty for extending gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences.beta12orEarlierSequence identitybeta12orEarlierSequence identity is the number (%) of matches (identical characters) in positions from an alignment of two molecular sequences.Sequence similarityData Type is float probably.beta12orEarlierSequence similarity is the similarity (expressed as a percentage) of two molecular sequences calculated from their alignment, a scoring matrix for scoring characters substitutions and penalties for gap insertion and extension.Sequence alignment metadata (quality report)trueData on molecular sequence alignment quality (estimated accuracy).beta12orEarlierbeta12orEarlierSequence alignment report (site conservation)trueData on character conservation in a molecular sequence alignment.beta12orEarlierThis is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. Use this concept for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc.1.4Sequence alignment report (site correlation)1.4truebeta12orEarlierData on correlations between sites in a molecular sequence alignment, typically to identify possible covarying positions and predict contacts or structural constraints in protein structures.Sequence-profile alignment (Domainatrix signature)Alignment of molecular sequences to a Domainatrix signature (representing a sequence alignment).beta12orEarlierbeta12orEarliertrueSequence-profile alignment (HMM)beta12orEarliertrue1.5Alignment of molecular sequence(s) to a hidden Markov model(s).Sequence-profile alignment (fingerprint)truebeta12orEarlier1.5Alignment of molecular sequences to a protein fingerprint from the PRINTS database.Phylogenetic continuous quantitative dataPhylogenetic continuous quantitative charactersbeta12orEarlierQuantitative traitsContinuous quantitative data that may be read during phylogenetic tree calculation.Phylogenetic discrete dataDiscrete charactersbeta12orEarlierDiscretely coded charactersCharacter data with discrete states that may be read during phylogenetic tree calculation.Phylogenetic discrete statesPhylogenetic character cliquesbeta12orEarlierOne or more cliques of mutually compatible characters that are generated, for example from analysis of discrete character data, and are used to generate a phylogeny.Phylogenetic report (cliques)Phylogenetic invariantsPhylogenetic invariants data for testing alternative tree topologies.beta12orEarlierPhylogenetic report (invariants)Phylogenetic reportA report of data concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees.1.5This is a broad data type and is used for example for reports on confidence, shape or stratigraphic (age) data derived from phylogenetic tree analysis.beta12orEarliertrueDNA substitution modelSubstitution modelSequence alignment report (DNA substitution model)beta12orEarlierPhylogenetic tree report (DNA substitution model)A model of DNA substitution that explains a DNA sequence alignment, derived from phylogenetic tree analysis.Phylogenetic tree report (tree shape)1.4truebeta12orEarlierData about the shape of a phylogenetic tree.Phylogenetic tree report (tree evaluation)Data on the confidence of a phylogenetic tree.beta12orEarliertrue1.4Phylogenetic tree distancesPhylogenetic tree report (tree distances)Distances, such as Branch Score distance, between two or more phylogenetic trees.beta12orEarlierPhylogenetic tree report (tree stratigraphic)beta12orEarlierMolecular clock and stratigraphic (age) data derived from phylogenetic tree analysis.true1.4Phylogenetic character contrastsIndependent contrasts for characters used in a phylogenetic tree, or covariances, regressions and correlations between characters for those contrasts.beta12orEarlierPhylogenetic report (character contrasts)Comparison matrix (integers)beta12orEarliertruebeta12orEarlierMatrix of integer numbers for sequence comparison.Comparison matrix (floats)beta12orEarlierMatrix of floating point numbers for sequence comparison.beta12orEarliertrueComparison matrix (nucleotide)Matrix of integer or floating point numbers for nucleotide comparison.beta12orEarlierNucleotide substitution matrixComparison matrix (amino acid)Matrix of integer or floating point numbers for amino acid comparison.Amino acid substitution matrixbeta12orEarlierAmino acid comparison matrixNucleotide comparison matrix (integers)beta12orEarliertrueMatrix of integer numbers for nucleotide comparison.beta12orEarlierNucleotide substitution matrix (integers)Nucleotide comparison matrix (floats)beta12orEarlierNucleotide substitution matrix (floats)Matrix of floating point numbers for nucleotide comparison.beta12orEarliertrueAmino acid comparison matrix (integers)Matrix of integer numbers for amino acid comparison.beta12orEarliertruebeta12orEarlierAmino acid comparison matrix (floats)truebeta12orEarlierMatrix of floating point numbers for amino acid comparison.beta12orEarlierProtein features report (membrane regions)1.8trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements.beta12orEarliertrueNucleic acid structurebeta12orEarlier3D coordinate and associated data for a nucleic acid tertiary (3D) structure.Protein structureProtein structures3D coordinate and associated data for a protein tertiary (3D) structure.beta12orEarlierProtein-ligand complexThe structure of a protein in complex with a ligand, typically a small molecule such as an enzyme substrate or cofactor, but possibly another macromolecule.beta12orEarlierThis includes interactions of proteins with atoms, ions and small molecules or macromolecules such as nucleic acids or other polypeptides. For stable inter-polypeptide interactions use 'Protein complex' instead.Carbohydrate structure3D coordinate and associated data for a carbohydrate (3D) structure.beta12orEarlierSmall molecule structure3D coordinate and associated data for the (3D) structure of a small molecule, such as any common chemical compound.beta12orEarlierCHEBI:23367DNA structurebeta12orEarlier3D coordinate and associated data for a DNA tertiary (3D) structure.RNA structure3D coordinate and associated data for an RNA tertiary (3D) structure.beta12orEarliertRNA structurebeta12orEarlier3D coordinate and associated data for a tRNA tertiary (3D) structure, including tmRNA, snoRNAs etc.Protein chainbeta12orEarlier3D coordinate and associated data for the tertiary (3D) structure of a polypeptide chain.Protein domain3D coordinate and associated data for the tertiary (3D) structure of a protein domain.beta12orEarlierProtein structure (all atoms)beta12orEarliertrue1.53D coordinate and associated data for a protein tertiary (3D) structure (all atoms).C-alpha trace3D coordinate and associated data for a protein tertiary (3D) structure (typically C-alpha atoms only).beta12orEarlierProtein structure (C-alpha atoms)C-beta atoms from amino acid side-chains may be included.Protein chain (all atoms)beta12orEarlier3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (all atoms).beta12orEarliertrueProtein chain (C-alpha atoms)truebeta12orEarlierbeta12orEarlier3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (typically C-alpha atoms only).C-beta atoms from amino acid side-chains may be included.Protein domain (all atoms)beta12orEarlier3D coordinate and associated data for a protein domain tertiary (3D) structure (all atoms).beta12orEarliertrueProtein domain (C-alpha atoms)C-beta atoms from amino acid side-chains may be included.truebeta12orEarlier3D coordinate and associated data for a protein domain tertiary (3D) structure (typically C-alpha atoms only).beta12orEarlierStructure alignment (pair)Pair structure alignmentAlignment (superimposition) of exactly two molecular tertiary (3D) structures.beta12orEarlierStructure alignment (multiple)beta12orEarliertruebeta12orEarlierAlignment (superimposition) of more than two molecular tertiary (3D) structures.Structure alignment (protein)Protein structure alignmentbeta12orEarlierAlignment (superimposition) of protein tertiary (3D) structures.Structure alignment (nucleic acid)beta12orEarlierNucleic acid structure alignmentAlignment (superimposition) of nucleic acid tertiary (3D) structures.Structure alignment (protein pair)1.12beta12orEarliertrueAlignment (superimposition) of exactly two protein tertiary (3D) structures.Multiple protein tertiary structure alignmenttruebeta12orEarlierAlignment (superimposition) of more than two protein tertiary (3D) structures.beta12orEarlierStructure alignment (protein all atoms)1.5Alignment (superimposition) of protein tertiary (3D) structures (all atoms considered).truebeta12orEarlierStructure alignment (protein C-alpha atoms)Alignment (superimposition) of protein tertiary (3D) structures (typically C-alpha atoms only considered).1.5C-beta atoms from amino acid side-chains may be considered.beta12orEarliertruePairwise protein tertiary structure alignment (all atoms)beta12orEarliertruebeta12orEarlierAlignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered).Pairwise protein tertiary structure alignment (C-alpha atoms)Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered).beta12orEarlierC-beta atoms from amino acid side-chains may be included.truebeta12orEarlierMultiple protein tertiary structure alignment (all atoms)beta12orEarliertruebeta12orEarlierAlignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered).Multiple protein tertiary structure alignment (C-alpha atoms)Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered).beta12orEarlierC-beta atoms from amino acid side-chains may be included.truebeta12orEarlierStructure alignment (nucleic acid pair)1.12beta12orEarliertrueAlignment (superimposition) of exactly two nucleic acid tertiary (3D) structures.Multiple nucleic acid tertiary structure alignmentAlignment (superimposition) of more than two nucleic acid tertiary (3D) structures.beta12orEarliertruebeta12orEarlierStructure alignment (RNA)beta12orEarlierRNA structure alignmentAlignment (superimposition) of RNA tertiary (3D) structures.Structural transformation matrixMatrix to transform (rotate/translate) 3D coordinates, typically the transformation necessary to superimpose two molecular structures.beta12orEarlierDaliLite hit tablebeta12orEarliertruebeta12orEarlierDaliLite hit table of protein chain tertiary structure alignment data.The significant and top-scoring hits for regions of the compared structures is shown. Data such as Z-Scores, number of aligned residues, root-mean-square deviation (RMSD) of atoms and sequence identity are given.Molecular similarity scoretruebeta12orEarlierbeta12orEarlierA score reflecting structural similarities of two molecules.Root-mean-square deviationRMSDRoot-mean-square deviation (RMSD) is calculated to measure the average distance between superimposed macromolecular coordinates.beta12orEarlierTanimoto similarity scorebeta12orEarlierA measure of the similarity between two ligand fingerprints.A ligand fingerprint is derived from ligand structural data from a Protein DataBank file. It reflects the elements or groups present or absent, covalent bonds and bond orders and the bonded environment in terms of SATIS codes and BLEEP atom types.3D-1D scoring matrixA matrix of 3D-1D scores reflecting the probability of amino acids to occur in different tertiary structural environments.beta12orEarlierAmino acid indexA table of 20 numerical values which quantify a property (e.g. physicochemical or biochemical) of the common amino acids.beta12orEarlierAmino acid index (chemical classes)Chemical classes (amino acids)beta12orEarlierChemical classification (small, aliphatic, aromatic, polar, charged etc) of amino acids.Amino acid pair-wise contact potentialsStatistical protein contact potentials.beta12orEarlierContact potentials (amino acid pair-wise)Amino acid index (molecular weight)Molecular weight (amino acids)beta12orEarlierMolecular weights of amino acids.Amino acid index (hydropathy)beta12orEarlierHydrophobic, hydrophilic or charge properties of amino acids.Hydropathy (amino acids)Amino acid index (White-Wimley data)White-Wimley data (amino acids)Experimental free energy values for the water-interface and water-octanol transitions for the amino acids.beta12orEarlierAmino acid index (van der Waals radii)beta12orEarlierVan der Waals radii of atoms for different amino acid residues.van der Waals radii (amino acids)Enzyme reportAn informative report on a specific enzyme.beta12orEarliertrue1.5Restriction enzyme reporttrueAn informative report on a specific restriction enzyme such as enzyme reference data.This might include name of enzyme, organism, isoschizomers, methylation, source, suppliers, literature references, or data on restriction enzyme patterns such as name of enzyme, recognition site, length of pattern, number of cuts made by enzyme, details of blunt or sticky end cut etc.1.5beta12orEarlierPeptide molecular weightsList of molecular weight(s) of one or more proteins or peptides, for example cut by proteolytic enzymes or reagents.beta12orEarlierThe report might include associated data such as frequency of peptide fragment molecular weights.Peptide hydrophobic momentReport on the hydrophobic moment of a polypeptide sequence.beta12orEarlierHydrophobic moment is a peptides hydrophobicity measured for different angles of rotation.Protein aliphatic indexThe aliphatic index of a protein.The aliphatic index is the relative protein volume occupied by aliphatic side chains.beta12orEarlierProtein sequence hydropathy plotbeta12orEarlierHydrophobic moment is a peptides hydrophobicity measured for different angles of rotation.A protein sequence with annotation on hydrophobic or hydrophilic / charged regions, hydrophobicity plot etc.Protein charge plotbeta12orEarlierA plot of the mean charge of the amino acids within a window of specified length as the window is moved along a protein sequence.Protein solubilitybeta12orEarlierProtein solubility dataThe solubility or atomic solvation energy of a protein sequence or structure.Protein crystallizabilityData on the crystallizability of a protein sequence.beta12orEarlierProtein crystallizability dataProtein globularitybeta12orEarlierData on the stability, intrinsic disorder or globularity of a protein sequence.Protein globularity dataProtein titration curvebeta12orEarlierThe titration curve of a protein.Protein isoelectric pointbeta12orEarlierThe isoelectric point of one proteins.Protein pKa valuebeta12orEarlierThe pKa value of a protein.Protein hydrogen exchange rateThe hydrogen exchange rate of a protein.beta12orEarlierProtein extinction coefficientThe extinction coefficient of a protein.beta12orEarlierProtein optical densityThe optical density of a protein.beta12orEarlierProtein subcellular localisationProtein report (subcellular localisation)truebeta12orEarlierAn informative report on protein subcellular localisation (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or destination (exported / extracellular proteins).beta13Peptide immunogenicity dataThis includes data on peptide ligands that elicit an immune response (immunogens), allergic cross-reactivity, predicted antigenicity (Hopp and Woods plot) etc. These data are useful in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data.Peptide immunogenicity reportAn report on allergenicity / immunogenicity of peptides and proteins.Peptide immunogenicitybeta12orEarlierMHC peptide immunogenicity reportA report on the immunogenicity of MHC class I or class II binding peptides.beta12orEarliertruebeta13Protein structure reportAnnotation about, or structural information derived from, one or more specific protein 3D structure(s) or structural domains.Protein report (structure)Protein structure-derived reportbeta12orEarlierThis includes for example reports on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure, protein flexibility or motion, and protein architecture (spatial arrangement of secondary structure).Protein property (structural)Protein structural propertyProtein structure report (domain)Protein structural quality reportProtein property (structural quality)Report on the quality of a protein three-dimensional model.Protein structure validation reportProtein structure report (quality evaluation)Protein report (structural quality)Model validation might involve checks for atomic packing, steric clashes, agreement with electron density maps etc.beta12orEarlierProtein non-covalent interactions report1.12truebeta12orEarlierData on inter-atomic or inter-residue contacts, distances and interactions in protein structure(s) or on the interactions of protein atoms or residues with non-protein groups.Protein flexibility or motion reportInformative report on flexibility or motion of a protein structure.This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.beta12orEarlier1.4trueProtein solvent accessibility reportbeta12orEarlierThis is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. This concept covers definitions of the protein surface, interior and interfaces, accessible and buried residues, surface accessible pockets, interior inaccessible cavities etc.Data on the solvent accessible or buried surface area of a protein structure.Protein surface report1.4Data on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure.trueThis is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.beta12orEarlierRamachandran plotPhi/psi angle data or a Ramachandran plot of a protein structure.beta12orEarlierProtein dipole momentbeta12orEarlierData on the net charge distribution (dipole moment) of a protein structure.Protein distance matrixbeta12orEarlierA matrix of distances between amino acid residues (for example the C-alpha atoms) in a protein structure.Protein contact mapbeta12orEarlierAn amino acid residue contact map for a protein structure.Protein residue 3D clusterbeta12orEarlierReport on clusters of contacting residues in protein structures such as a key structural residue network.Protein hydrogen bondsPatterns of hydrogen bonding in protein structures.beta12orEarlierProtein non-canonical interactionstruebeta12orEarlierNon-canonical atomic interactions in protein structures.1.4CATH node1.5The report (for example http://www.cathdb.info/cathnode/1.10.10.10) includes CATH code (of the node and upper levels in the hierarchy), classification text (of appropriate levels in hierarchy), list of child nodes, representative domain and other relevant data and links.beta12orEarliertrueInformation on a node from the CATH database.SCOP nodeInformation on a node from the SCOP database.1.5truebeta12orEarlierEMBASSY domain classificationbeta12orEarliertruebeta12orEarlierAn EMBASSY domain classification file (DCF) of classification and other data for domains from SCOP or CATH, in EMBL-like format.CATH class1.5beta12orEarliertrueInformation on a protein 'class' node from the CATH database.CATH architecturetruebeta12orEarlierInformation on a protein 'architecture' node from the CATH database.1.5CATH topology1.5Information on a protein 'topology' node from the CATH database.truebeta12orEarlierCATH homologous superfamilytruebeta12orEarlierInformation on a protein 'homologous superfamily' node from the CATH database.1.5CATH structurally similar group1.5beta12orEarliertrueInformation on a protein 'structurally similar group' node from the CATH database.CATH functional categorybeta12orEarliertrueInformation on a protein 'functional category' node from the CATH database.1.5Protein fold recognition reportbeta12orEarliertruebeta12orEarlierMethods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH.A report on known protein structural domains or folds that are recognised (identified) in protein sequence(s).Protein-protein interaction report1.8protein-protein interaction(s), including interactions between protein domains.beta12orEarliertrueProtein-ligand interaction reportProtein-drug interaction reportbeta12orEarlierAn informative report on protein-ligand (small molecule) interaction(s).Protein-nucleic acid interactions report1.8protein-DNA/RNA interaction(s).truebeta12orEarlierNucleic acid melting profilebeta12orEarlierData on the dissociation characteristics of a double-stranded nucleic acid molecule (DNA or a DNA/RNA hybrid) during heating.Nucleic acid stability profileA melting (stability) profile calculated the free energy required to unwind and separate the nucleic acid strands, plotted for sliding windows over a sequence.Nucleic acid enthalpyEnthalpy of hybridised or double stranded nucleic acid (DNA or RNA/DNA).beta12orEarlierNucleic acid entropyEntropy of hybridised or double stranded nucleic acid (DNA or RNA/DNA).beta12orEarlierNucleic acid melting temperatureMelting temperature of hybridised or double stranded nucleic acid (DNA or RNA/DNA).truebeta12orEarlierbeta12orEarlierNucleic acid stitch profileStitch profile of hybridised or double stranded nucleic acid (DNA or RNA/DNA).beta12orEarlierA stitch profile diagram shows partly melted DNA conformations (with probabilities) at a range of temperatures. For example, a stitch profile might show possible loop openings with their location, size, probability and fluctuations at a given temperature.DNA base pair stacking energies databeta12orEarlierDNA base pair stacking energies data.DNA base pair twist angle dataDNA base pair twist angle data.beta12orEarlierDNA base trimer roll angles dataDNA base trimer roll angles data.beta12orEarlierVienna RNA parametersbeta12orEarliertruebeta12orEarlierRNA parameters used by the Vienna package.Vienna RNA structure constraintstruebeta12orEarlierbeta12orEarlierStructure constraints used by the Vienna package.Vienna RNA concentration databeta12orEarlierRNA concentration data used by the Vienna package.truebeta12orEarlierVienna RNA calculated energyRNA calculated energy data generated by the Vienna package.truebeta12orEarlierbeta12orEarlierBase pairing probability matrix dotplotDotplot of RNA base pairing probability matrix.beta12orEarlierSuch as generated by the Vienna package.Nucleic acid folding reportRNA secondary structure folding probablitiesbeta12orEarlierRNA secondary structure folding classificationNucleic acid report (folding model)Nucleic acid report (folding)A report on an analysis of RNA/DNA folding, minimum folding energies for DNA or RNA sequences, energy landscape of RNA mutants etc.Codon usage tableTable of codon usage data calculated from one or more nucleic acid sequences.beta12orEarlierA codon usage table might include the codon usage table name, optional comments and a table with columns for codons and corresponding codon usage data. A genetic code can be extracted from or represented by a codon usage table.Genetic codeA genetic code for an organism.A genetic code need not include detailed codon usage information.beta12orEarlierCodon adaptation indextruebeta12orEarlierA simple measure of synonymous codon usage bias often used to predict gene expression levels.beta12orEarlierCodon usage bias plotSynonymous codon usage statistic plotbeta12orEarlierA plot of the synonymous codon usage calculated for windows over a nucleotide sequence.Nc statistictruebeta12orEarlierbeta12orEarlierThe effective number of codons used in a gene sequence. This reflects how far codon usage of a gene departs from equal usage of synonymous codons.Codon usage fraction differenceThe differences in codon usage fractions between two codon usage tables.beta12orEarlierPharmacogenomic test reportbeta12orEarlierThe report might correlate gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity.Data on the influence of genotype on drug response.Disease reportAn informative report on a specific disease.For example, an informative report on a specific tumor including nature and origin of the sample, anatomic site, organ or tissue, tumor type, including morphology and/or histologic type, and so on.beta12orEarlierLinkage disequilibrium (report)A report on linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome).truebeta12orEarlier1.8HeatmapHeat mapA heat map is a table where rows and columns correspond to different genes and contexts (for example, cells or samples) and the cell color represents the level of expression of a gene that context.beta12orEarlierA graphical 2D tabular representation of gene expression data, typically derived from a DNA microarray experiment.Affymetrix probe sets library filebeta12orEarliertruebeta12orEarlierAffymetrix library file of information about which probes belong to which probe set.Affymetrix probe sets information library filetruebeta12orEarlierAffymetrix library file of information about the probe sets such as the gene name with which the probe set is associated.beta12orEarlierGIN fileMolecular weights standard fingerprint1.12Standard protonated molecular masses from trypsin (modified porcine trypsin, Promega) and keratin peptides, used in EMBOSS.truebeta12orEarlierMetabolic pathway reportA report typically including a map (diagram) of a metabolic pathway.truebeta12orEarlier1.8This includes carbohydrate, energy, lipid, nucleotide, amino acid, glycan, PK/NRP, cofactor/vitamin, secondary metabolite, xenobiotics etc.Genetic information processing pathway reportgenetic information processing pathways.1.8truebeta12orEarlierEnvironmental information processing pathway reporttruebeta12orEarlierenvironmental information processing pathways.1.8Signal transduction pathway reportbeta12orEarliertrue1.8A report typically including a map (diagram) of a signal transduction pathway.Cellular process pathways report1.8beta12orEarliertrueTopic concernning cellular process pathways.Disease pathway or network reportdisease pathways, typically of human disease.1.8truebeta12orEarlierDrug structure relationship mapbeta12orEarlierA report typically including a map (diagram) of drug structure relationships.Protein interaction networksbeta12orEarliertrue1.8networks of protein interactions.MIRIAM datatype1.5A MIRIAM entry describes a MIRIAM data type including the official name, synonyms, root URI, identifier pattern (regular expression applied to a unique identifier of the data type) and documentation. Each data type can be associated with several resources. Each resource is a physical location of a service (typically a database) providing information on the elements of a data type. Several resources may exist for each data type, provided the same (mirrors) or different information. MIRIAM provides a stable and persistent reference to its data types.An entry (data type) from the Minimal Information Requested in the Annotation of Biochemical Models (MIRIAM) database of data resources.truebeta12orEarlierE-valueA simple floating point number defining the lower or upper limit of an expectation value (E-value).beta12orEarlierAn expectation value (E-Value) is the expected number of observations which are at least as extreme as observations expected to occur by random chance. The E-value describes the number of hits with a given score or better that are expected to occur at random when searching a database of a particular size. It decreases exponentially with the score (S) of a hit. A low E value indicates a more significant score.Expectation valueZ-valueThe z-value is the number of standard deviations a data value is above or below a mean value.A z-value might be specified as a threshold for reporting hits from database searches.beta12orEarlierP-valueA z-value might be specified as a threshold for reporting hits from database searches.The P-value is the probability of obtaining by random chance a result that is at least as extreme as an observed result, assuming a NULL hypothesis is true.beta12orEarlierDatabase version informationbeta12orEarlierInformation on a database (or ontology) version, for example name, version number and release date.true1.5Tool version information1.5truebeta12orEarlierInformation on an application version, for example name, version number and release date.CATH version informationbeta12orEarlierbeta12orEarliertrueInformation on a version of the CATH database.Swiss-Prot to PDB mappingbeta12orEarlierbeta12orEarliertrueCross-mapping of Swiss-Prot codes to PDB identifiers.Sequence database cross-referencestrueCross-references from a sequence record to other databases.beta12orEarlierbeta12orEarlierJob status1.5beta12orEarlierValues for EBI services are 'DONE' (job has finished and the results can then be retrieved), 'ERROR' (the job failed or no results where found), 'NOT_FOUND' (the job id is no longer available; job results might be deleted, 'PENDING' (the job is in a queue waiting processing), 'RUNNING' (the job is currently being processed).trueMetadata on the status of a submitted job.Job IDtrueThe (typically numeric) unique identifier of a submitted job.beta12orEarlier1.0Job typebeta12orEarlierA label (text token) describing the type of job, for example interactive or non-interactive.true1.5Tool logA report of tool-specific metadata on some analysis or process performed, for example a log of diagnostic or error messages.true1.5beta12orEarlierDaliLite log filebeta12orEarlierbeta12orEarlierDaliLite log file describing all the steps taken by a DaliLite alignment of two protein structures.trueSTRIDE log fileSTRIDE log file.beta12orEarliertruebeta12orEarlierNACCESS log filebeta12orEarliertruebeta12orEarlierNACCESS log file.EMBOSS wordfinder log fileEMBOSS wordfinder log file.truebeta12orEarlierbeta12orEarlierEMBOSS domainatrix log filetruebeta12orEarlierEMBOSS (EMBASSY) domainatrix application log file.beta12orEarlierEMBOSS sites log filebeta12orEarlierEMBOSS (EMBASSY) sites application log file.truebeta12orEarlierEMBOSS supermatcher error fileEMBOSS (EMBASSY) supermatcher error file.beta12orEarlierbeta12orEarliertrueEMBOSS megamerger log filebeta12orEarliertruebeta12orEarlierEMBOSS megamerger log file.EMBOSS whichdb log fileEMBOSS megamerger log file.beta12orEarliertruebeta12orEarlierEMBOSS vectorstrip log fileEMBOSS vectorstrip log file.beta12orEarliertruebeta12orEarlierUsernameA username on a computer system.beta12orEarlierPasswordbeta12orEarlierA password on a computer system.Email addressMoby:EmailAddressMoby:EmailA valid email address of an end-user.beta12orEarlierPerson namebeta12orEarlierThe name of a person.Number of iterationsNumber of iterations of an algorithm.1.5beta12orEarliertrueNumber of output entitiesbeta12orEarliertrueNumber of entities (for example database hits, sequences, alignments etc) to write to an output file.1.5Hit sort orderControls the order of hits (reported matches) in an output file from a database search.beta12orEarliertruebeta12orEarlierDrug reportDrug annotationAn informative report on a specific drug.beta12orEarlierPhylogenetic tree imageAn image (for viewing or printing) of a phylogenetic tree including (typically) a plot of rooted or unrooted phylogenies, cladograms, circular trees or phenograms and associated information.beta12orEarlierSee also 'Phylogenetic tree'RNA secondary structure imageImage of RNA secondary structure, knots, pseudoknots etc.beta12orEarlierProtein secondary structure imageImage of protein secondary structure.beta12orEarlierStructure imagebeta12orEarlierImage of one or more molecular tertiary (3D) structures.Sequence alignment imageImage of two or more aligned molecular sequences possibly annotated with alignment features.beta12orEarlierChemical structure imagebeta12orEarlierSmall molecule structure imageAn image of the structure of a small chemical compound.The molecular identifier and formula are typically included.Fate map A fate map is a plan of early stage of an embryo such as a blastula, showing areas that are significance to development.beta12orEarlierMicroarray spots imageAn image of spots from a microarray experiment.beta12orEarlierBioPax termbeta12orEarliertruebeta12orEarlierA term from the BioPax ontology.GOA term definition from The Gene Ontology (GO).truebeta12orEarlierbeta12orEarlierMeSHA term from the MeSH vocabulary.truebeta12orEarlierbeta12orEarlierHGNCA term from the HGNC controlled vocabulary.beta12orEarlierbeta12orEarliertrueNCBI taxonomy vocabularyA term from the NCBI taxonomy vocabulary.beta12orEarliertruebeta12orEarlierPlant ontology termA term from the Plant Ontology (PO).beta12orEarliertruebeta12orEarlierUMLSA term from the UMLS vocabulary.beta12orEarliertruebeta12orEarlierFMAClassifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented.beta12orEarlierA term from Foundational Model of Anatomy.truebeta12orEarlierEMAPtruebeta12orEarlierA term from the EMAP mouse ontology.beta12orEarlierChEBIA term from the ChEBI ontology.truebeta12orEarlierbeta12orEarlierMGEDbeta12orEarlierA term from the MGED ontology.truebeta12orEarliermyGridbeta12orEarlierThe ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services.beta12orEarliertrueA term from the myGrid ontology.GO (biological process)A term definition for a biological process from the Gene Ontology (GO).beta12orEarliertruebeta12orEarlierData Type is an enumerated string.GO (molecular function)beta12orEarliertrueData Type is an enumerated string.beta12orEarlierA term definition for a molecular function from the Gene Ontology (GO).GO (cellular component)Data Type is an enumerated string.A term definition for a cellular component from the Gene Ontology (GO).beta12orEarliertruebeta12orEarlierOntology relation typeA relation type defined in an ontology.1.5beta12orEarliertrueOntology concept definitionThe definition of a concept from an ontology.Ontology class definitionbeta12orEarlierOntology concept commenttrue1.4beta12orEarlierA comment on a concept from an ontology.Ontology concept referenceReference for a concept from an ontology.beta12orEarliertruebeta12orEarlierdoc2loc document informationInformation on a published article provided by the doc2loc program.beta12orEarlierThe doc2loc output includes the url, format, type and availability code of a document for every service provider.beta12orEarliertruePDB residue numberWHATIF: pdb_numberPDBML:PDB_residue_noA residue identifier (a string) from a PDB file.beta12orEarlierAtomic coordinatebeta12orEarlierCartesian coordinateCartesian coordinate of an atom (in a molecular structure).Atomic x coordinateCartesian x coordinatePDBML:_atom_site.Cartn_x in PDBMLbeta12orEarlierWHATIF: PDBx_Cartn_xCartesian x coordinate of an atom (in a molecular structure).Atomic y coordinatebeta12orEarlierWHATIF: PDBx_Cartn_yPDBML:_atom_site.Cartn_y in PDBMLCartesian y coordinate of an atom (in a molecular structure).Cartesian y coordinateAtomic z coordinateCartesian z coordinate of an atom (in a molecular structure).Cartesian z coordinatebeta12orEarlierPDBML:_atom_site.Cartn_zWHATIF: PDBx_Cartn_zPDB atom nameWHATIF: PDBx_auth_atom_idWHATIF: PDBx_type_symbolIdentifier (a string) of a specific atom from a PDB file for a molecular structure.WHATIF: atom_typeWHATIF: alternate_atombeta12orEarlierPDBML:pdbx_PDB_atom_nameProtein atomAtom dataThis is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.Data on a single atom from a protein structure.CHEBI:33250beta12orEarlierProtein residuebeta12orEarlierData on a single amino acid residue position in a protein structure.This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.ResidueAtom nameName of an atom.beta12orEarlierPDB residue nameThree-letter amino acid residue names as used in PDB files.beta12orEarlierWHATIF: typePDB model numberIdentifier of a model structure from a PDB file.beta12orEarlierPDBML:pdbx_PDB_model_numWHATIF: model_numberModel numberCATH domain reportbeta13Summary of domain classification information for a CATH domain.The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links.truebeta12orEarlierCATH representative domain sequences (ATOM)FASTA sequence database (based on ATOM records in PDB) for CATH domains (clustered at different levels of sequence identity).beta12orEarliertruebeta12orEarlierCATH representative domain sequences (COMBS)FASTA sequence database (based on COMBS sequence data) for CATH domains (clustered at different levels of sequence identity).truebeta12orEarlierbeta12orEarlierCATH domain sequences (ATOM)FASTA sequence database for all CATH domains (based on PDB ATOM records).truebeta12orEarlierbeta12orEarlierCATH domain sequences (COMBS)truebeta12orEarlierbeta12orEarlierFASTA sequence database for all CATH domains (based on COMBS sequence data).Sequence versionbeta12orEarlierSequence version informationInformation on an molecular sequence version.Scorebeta12orEarlierA numerical value, that is some type of scored value arising for example from a prediction method.Protein report (function)truebeta13Report on general functional properties of specific protein(s).beta12orEarlierFor properties that can be mapped to a sequence, use 'Sequence report' instead.Gene name (ASPGD)1.3Name of a gene from Aspergillus Genome Database.beta12orEarliertruehttp://www.geneontology.org/doc/GO.xrf_abbs:ASPGD_LOCUSGene name (CGD)Name of a gene from Candida Genome Database.http://www.geneontology.org/doc/GO.xrf_abbs:CGD_LOCUS1.3truebeta12orEarlierGene name (dictyBase)Name of a gene from dictyBase database.beta12orEarliertrue1.3http://www.geneontology.org/doc/GO.xrf_abbs:dictyBaseGene name (EcoGene primary)EcoGene primary gene namehttp://www.geneontology.org/doc/GO.xrf_abbs:ECOGENE_Gtruebeta12orEarlierPrimary name of a gene from EcoGene Database.1.3Gene name (MaizeGDB)http://www.geneontology.org/doc/GO.xrf_abbs:MaizeGDB_Locus1.3beta12orEarliertrueName of a gene from MaizeGDB (maize genes) database.Gene name (SGD)http://www.geneontology.org/doc/GO.xrf_abbs:SGD_LOCUSName of a gene from Saccharomyces Genome Database.1.3beta12orEarliertrueGene name (TGD)http://www.geneontology.org/doc/GO.xrf_abbs:TGD_LOCUStrueName of a gene from Tetrahymena Genome Database.beta12orEarlier1.3Gene name (CGSC)http://www.geneontology.org/doc/GO.xrf_abbs: CGSCSymbol of a gene from E.coli Genetic Stock Center.truebeta12orEarlier1.3Gene name (HGNC)1.3beta12orEarlierhttp://www.geneontology.org/doc/GO.xrf_abbs: HGNC_geneHGNC:[0-9]{1,5}trueSymbol of a gene approved by the HUGO Gene Nomenclature Committee.Gene name (MGD)1.3Symbol of a gene from the Mouse Genome Database.MGI:[0-9]+http://www.geneontology.org/doc/GO.xrf_abbs: MGDtruebeta12orEarlierGene name (Bacillus subtilis)truebeta12orEarlier1.3http://www.geneontology.org/doc/GO.xrf_abbs: SUBTILISTGSymbol of a gene from Bacillus subtilis Genome Sequence Project.Gene ID (PlasmoDB)beta12orEarlierIdentifier of a gene from PlasmoDB Plasmodium Genome Resource.http://www.geneontology.org/doc/GO.xrf_abbs: ApiDB_PlasmoDBGene ID (EcoGene)Identifier of a gene from EcoGene Database.EcoGene Accessionbeta12orEarlierEcoGene IDGene ID (FlyBase)beta12orEarlierhttp://www.geneontology.org/doc/GO.xrf_abbs: FBhttp://www.geneontology.org/doc/GO.xrf_abbs: FlyBaseGene identifier from FlyBase database.Gene ID (GeneDB Glossina morsitans)Gene identifier from Glossina morsitans GeneDB database.truebeta12orEarlierbeta13Gene ID (GeneDB Leishmania major)beta13beta12orEarliertrueGene identifier from Leishmania major GeneDB database.Gene ID (GeneDB Plasmodium falciparum)Gene identifier from Plasmodium falciparum GeneDB database.http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Pfalciparumbeta13truebeta12orEarlierGene ID (GeneDB Schizosaccharomyces pombe)beta13truebeta12orEarlierhttp://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_SpombeGene identifier from Schizosaccharomyces pombe GeneDB database.Gene ID (GeneDB Trypanosoma brucei)Gene identifier from Trypanosoma brucei GeneDB database.http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Tbruceitruebeta12orEarlierbeta13Gene ID (Gramene)http://www.geneontology.org/doc/GO.xrf_abbs: GR_genehttp://www.geneontology.org/doc/GO.xrf_abbs: GR_GENEbeta12orEarlierGene identifier from Gramene database.Gene ID (Virginia microbial)http://www.geneontology.org/doc/GO.xrf_abbs: PAMGO_VMDGene identifier from Virginia Bioinformatics Institute microbial database.beta12orEarlierhttp://www.geneontology.org/doc/GO.xrf_abbs: VMDGene ID (SGN)http://www.geneontology.org/doc/GO.xrf_abbs: SGNGene identifier from Sol Genomics Network.beta12orEarlierGene ID (WormBase)http://www.geneontology.org/doc/GO.xrf_abbs: WBWBGene[0-9]{8}beta12orEarlierGene identifier used by WormBase database.http://www.geneontology.org/doc/GO.xrf_abbs: WormBaseGene synonymAny name (other than the recommended one) for a gene.truebeta12orEarlierbeta12orEarlierORF namebeta12orEarlierThe name of an open reading frame attributed by a sequencing project.Sequence assembly componentA component of a larger sequence assembly.beta12orEarliertruebeta12orEarlierChromosome annotation (aberration)A report on a chromosome aberration such as abnormalities in chromosome structure.beta12orEarliertruebeta12orEarlierClone IDAn identifier of a clone (cloned molecular sequence) from a database.beta12orEarlierPDB insertion codePDBML:pdbx_PDB_ins_codeWHATIF: insertion_codeAn insertion code (part of the residue number) for an amino acid residue from a PDB file.beta12orEarlierAtomic occupancyThe fraction of an atom type present at a site in a molecular structure.beta12orEarlierWHATIF: PDBx_occupancyThe sum of the occupancies of all the atom types at a site should not normally significantly exceed 1.0.Isotropic B factorbeta12orEarlierIsotropic B factor (atomic displacement parameter) for an atom from a PDB file.WHATIF: PDBx_B_iso_or_equivDeletion mapA cytogenetic map showing chromosome banding patterns in mutant cell lines relative to the wild type.A cytogenetic map is built from a set of mutant cell lines with sub-chromosomal deletions and a reference wild-type line ('genome deletion panel'). The panel is used to map markers onto the genome by comparing mutant to wild-type banding patterns. Markers are linked (occur in the same deleted region) if they share the same banding pattern (presence or absence) as the deletion panel.beta12orEarlierDeletion-based cytogenetic mapQTL mapbeta12orEarlierQuantitative trait locus mapA genetic map which shows the approximate location of quantitative trait loci (QTL) between two or more markers.Haplotype mapMoby:Haplotyping_Study_objA map of haplotypes in a genome or other sequence, describing common patterns of genetic variation.beta12orEarlierMap set databeta12orEarlierMoby:GCP_CorrelatedMapSetMoby:GCP_CorrelatedLinkageMapSetData describing a set of multiple genetic or physical maps, typically sharing a common set of features which are mapped.Map featurebeta12orEarlierA feature which may mapped (positioned) on a genetic or other type of map.Mappable features may be based on Gramene's notion of map features; see http://www.gramene.org/db/cmap/feature_type_info.beta12orEarliertrueMap typeMap types may be based on Gramene's notion of a map type; see http://www.gramene.org/db/cmap/map_type_info.1.5beta12orEarliertrueA designation of the type of map (genetic map, physical map, sequence map etc) or map set.Protein fold nameThe name of a protein fold.beta12orEarlierTaxonMoby:PotentialTaxonFor a complete list of taxonomic ranks see https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary.beta12orEarlierTaxonomy rankTaxonomic rankThe name of a group of organisms belonging to the same taxonomic rank.Moby:BriefTaxonConceptOrganism identifierbeta12orEarlierA unique identifier of a (group of) organisms.Genus nameThe name of a genus of organism.beta12orEarlierTaxonomic classificationTaxonomic nameName components correspond to levels in a taxonomic hierarchy (e.g. 'Genus', 'Species', etc.) Meta information such as a reference where the name was defined and a date might be included.Moby:TaxonNamebeta12orEarlierMoby:GCP_TaxonMoby:iANT_organism-xmlTaxonomic informationThe full name for a group of organisms, reflecting their biological classification and (usually) conforming to a standard nomenclature.Moby:TaxonTCSMoby:TaxonScientificNameiHOP organism IDA unique identifier for an organism used in the iHOP database.Moby_namespace:iHOPorganismbeta12orEarlierGenbank common namebeta12orEarlierCommon name for an organism as used in the GenBank database.NCBI taxonThe name of a taxon from the NCBI taxonomy database.beta12orEarlierSynonymtruebeta12orEarlierbeta12orEarlierAn alternative for a word.Misspellingbeta12orEarliertruebeta12orEarlierA common misspelling of a word.Acronymbeta12orEarliertruebeta12orEarlierAn abbreviation of a phrase or word.Misnomerbeta12orEarliertrueA term which is likely to be misleading of its meaning.beta12orEarlierAuthor IDMoby:Authorbeta12orEarlierInformation on the authors of a published work.DragonDB author identifierAn identifier representing an author in the DragonDB database.beta12orEarlierAnnotated URIbeta12orEarlierMoby:DescribedLinkA URI along with annotation describing the data found at the address.UniProt keywordsA controlled vocabulary for words and phrases that can appear in the keywords field (KW line) of entries from the UniProt database.beta12orEarlierbeta12orEarliertrueGene ID (GeneFarm)Moby_namespace:GENEFARM_GeneIDbeta12orEarlierIdentifier of a gene from the GeneFarm database.Blattner numberbeta12orEarlierThe blattner identifier for a gene.Moby_namespace:Blattner_numberGene ID (MIPS Maize)truebeta12orEarlierbeta13Identifier for genetic elements in MIPS Maize database.Moby_namespace:MIPS_GE_MaizeGene ID (MIPS Medicago)Moby_namespace:MIPS_GE_MedicagoIdentifier for genetic elements in MIPS Medicago database.beta12orEarliertruebeta13Gene name (DragonDB)beta12orEarliertrueThe name of an Antirrhinum Gene from the DragonDB database.Moby_namespace:DragonDB_Gene1.3Gene name (Arabidopsis)A unique identifier for an Arabidopsis gene, which is an acronym or abbreviation of the gene name.1.3truebeta12orEarlieriHOP symbolbeta12orEarlierMoby_namespace:iHOPsymbolA unique identifier of a protein or gene used in the iHOP database.Gene name (GeneFarm)1.3GeneFarm gene IDbeta12orEarlierName of a gene from the GeneFarm database.trueLocus IDA unique name or other identifier of a genetic locus, typically conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome.Locus identifierLocus namebeta12orEarlierLocus ID (AGI)AGI locus codeAGI identifierhttp://www.geneontology.org/doc/GO.xrf_abbs:AGI_LocusCodebeta12orEarlierArabidopsis gene loci numberAGI IDAT[1-5]G[0-9]{5}Locus identifier for Arabidopsis Genome Initiative (TAIR, TIGR and MIPS databases)Locus ID (ASPGD)http://www.geneontology.org/doc/GO.xrf_abbs: ASPGDIdentifier for loci from ASPGD (Aspergillus Genome Database).beta12orEarlierhttp://www.geneontology.org/doc/GO.xrf_abbs: ASPGDIDLocus ID (MGG)Identifier for loci from Magnaporthe grisea Database at the Broad Institute.http://www.geneontology.org/doc/GO.xrf_abbs: Broad_MGGbeta12orEarlierLocus ID (CGD)Identifier for loci from CGD (Candida Genome Database).CGD locus identifierbeta12orEarlierCGDIDhttp://www.geneontology.org/doc/GO.xrf_abbs: CGDhttp://www.geneontology.org/doc/GO.xrf_abbs: CGDIDLocus ID (CMR)beta12orEarlierhttp://www.geneontology.org/doc/GO.xrf_abbs: JCVI_CMRLocus identifier for Comprehensive Microbial Resource at the J. Craig Venter Institute.http://www.geneontology.org/doc/GO.xrf_abbs: TIGR_CMRNCBI locus taghttp://www.geneontology.org/doc/GO.xrf_abbs: NCBI_locus_tagMoby_namespace:LocusIDLocus ID (NCBI)beta12orEarlierIdentifier for loci from NCBI database.Locus ID (SGD)beta12orEarlierSGDIDhttp://www.geneontology.org/doc/GO.xrf_abbs: SGDIDIdentifier for loci from SGD (Saccharomyces Genome Database).http://www.geneontology.org/doc/GO.xrf_abbs: SGDLocus ID (MMP)beta12orEarlierIdentifier of loci from Maize Mapping Project.Moby_namespace:MMP_LocusLocus ID (DictyBase)Identifier of locus from DictyBase (Dictyostelium discoideum).Moby_namespace:DDB_genebeta12orEarlierLocus ID (EntrezGene)Moby_namespace:EntrezGene_EntrezGeneIDbeta12orEarlierMoby_namespace:EntrezGene_IDIdentifier of a locus from EntrezGene database.Locus ID (MaizeGDB)Moby_namespace:MaizeGDB_Locusbeta12orEarlierIdentifier of locus from MaizeGDB (Maize genome database).Quantitative trait locustruebeta12orEarlierA stretch of DNA that is closely linked to the genes underlying a quantitative trait (a phenotype that varies in degree and depends upon the interactions between multiple genes and their environment).beta12orEarlierA QTL sometimes but does not necessarily correspond to a gene.Moby:SO_QTLGene ID (KOME)Identifier of a gene from the KOME database.Moby_namespace:GeneIdbeta12orEarlierLocus ID (Tropgene)Moby:Tropgene_locusIdentifier of a locus from the Tropgene database.beta12orEarlierAlignmentbeta12orEarlierAn alignment of molecular sequences, structures or profiles derived from them.Atomic propertyGeneral atomic propertyData for an atom (in a molecular structure).beta12orEarlierUniProt keywordhttp://www.geneontology.org/doc/GO.xrf_abbs: SP_KWbeta12orEarlierMoby_namespace:SP_KWA word or phrase that can appear in the keywords field (KW line) of entries from the UniProt database.Ordered locus nametruebeta12orEarlierA name for a genetic locus conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome.beta12orEarlierSequence coordinatesMoby:PositionMoby:GenePositionMoby:LocusA position in a map (for example a genetic map), either a single position (point) or a region / interval.Moby:MapPositionPDBML:_atom_site.idThis includes positions in genomes based on a reference sequence. A position may be specified for any mappable object, i.e. anything that may have positional information such as a physical position in a chromosome. Data might include sequence region name, strand, coordinate system name, assembly name, start position and end position.Map positionMoby:GCP_MapIntervalMoby:GCP_MapPositionMoby:GCP_MapPointLocusbeta12orEarlierSequence co-ordinatesMoby:HitPositionAmino acid propertybeta12orEarlierAmino acid dataData concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all amino acids.Annotationbeta12orEarliertruebeta13A human-readable collection of information which (typically) is generated or collated by hand and which describes a biological entity, phenomena or associated primary (e.g. sequence or structural) data, as distinct from the primary data itself and computer-generated reports derived from it.This is a broad data type and is used a placeholder for other, more specific types.Map dataA molecular map (genetic or physical), an attribute of such a map, or data extracted from or derived from the analysis of such a map.This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. It includes concepts that are best described as scientific text or closely concerned with or derived from text.beta12orEarlierMap attributeVienna RNA structural datatruebeta12orEarlierbeta12orEarlierData used by the Vienna RNA analysis package.Sequence mask parameter1.5beta12orEarliertrueData used to replace (mask) characters in a molecular sequence.Enzyme kinetics databeta12orEarlierData concerning chemical reaction(s) catalysed by enzyme(s).This is a broad data type and is used a placeholder for other, more specific types.Michaelis Menten plotbeta12orEarlierA plot giving an approximation of the kinetics of an enzyme-catalysed reaction, assuming simple kinetics (i.e. no intermediate or product inhibition, allostericity or cooperativity). It plots initial reaction rate to the substrate concentration (S) from which the maximum rate (vmax) is apparent.Hanes Woolf plotA plot based on the Michaelis Menten equation of enzyme kinetics plotting the ratio of the initial substrate concentration (S) against the reaction velocity (v).beta12orEarlierExperimental dataRaw data from or annotation on laboratory experiments.beta13This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.beta12orEarliertrueGenome version information1.5Information on a genome version.beta12orEarliertrueEvidenceTypically a statement about some data or results, including evidence or the source of a statement, which may include computational prediction, laboratory experiment, literature reference etc.beta12orEarlierSequence record lite1.8A molecular sequence and minimal metadata, typically an identifier of the sequence and/or a comment.beta12orEarliertrueSequencehttp://purl.org/biotop/biotop.owl#BioMolecularSequenceInformationbeta12orEarlierThis concept is a placeholder of concepts for primary sequence data including raw sequences and sequence records. It should not normally be used for derivatives such as sequence alignments, motifs or profiles.http://purl.bioontology.org/ontology/MSH/D008969SequencesOne or more molecular sequences, possibly with associated annotation.Nucleic acid sequence record (lite)truebeta12orEarlier1.8A nucleic acid sequence and minimal metadata, typically an identifier of the sequence and/or a comment.Protein sequence record (lite)Sequence record lite (protein)beta12orEarlier1.8A protein sequence and minimal metadata, typically an identifier of the sequence and/or a comment.trueReportYou can use this term by default for any textual report, in case you can't find another, more specific term. Reports may be generated automatically or collated by hand and can include metadata on the origin, source, history, ownership or location of some thing.Documentbeta12orEarlierhttp://semanticscience.org/resource/SIO_000148A human-readable collection of information including annotation on a biological entity or phenomena, computer-generated reports of analysis of primary data (e.g. sequence or structural), and metadata (data about primary data) or any other free (essentially unformatted) text, as distinct from the primary data itself.Molecular property (general)General data for a molecule.General molecular propertybeta12orEarlierStructural datatruebeta12orEarlierbeta13This is a broad data type and is used a placeholder for other, more specific types.Data concerning molecular structural data.Sequence motif (nucleic acid)A nucleotide sequence motif.beta12orEarlierRNA sequence motifNucleic acid sequence motifDNA sequence motifSequence motif (protein)Protein sequence motifAn amino acid sequence motif.beta12orEarlierSearch parametertruebeta12orEarlierSome simple value controlling a search operation, typically a search of a database.1.5Database search resultsSearch resultsDatabase hitsbeta12orEarlierA report of hits from searching a database of some type.Secondary structuretruebeta12orEarlierThe secondary structure assignment (predicted or real) of a nucleic acid or protein.1.5MatrixAn array of numerical values.ArrayThis is a broad data type and is used a placeholder for other, more specific types.beta12orEarlierAlignment dataData concerning, extracted from, or derived from the analysis of molecular alignment of some type.This is a broad data type and is used a placeholder for other, more specific types.truebeta12orEarlier1.8Nucleic acid reportbeta12orEarlierAn informative human-readable report about one or more specific nucleic acid molecules, derived from analysis of primary (sequence or structural) data.Structure reportStructure-derived reportAn informative report on general information, properties or features of one or more molecular tertiary (3D) structures.beta12orEarlierNucleic acid structure databeta12orEarlierThis includes reports on the stiffness, curvature, twist/roll data or other conformational parameters or properties.Nucleic acid structural propertyA report on nucleic acid structure-derived data, describing structural properties of a DNA molecule, or any other annotation or information about specific nucleic acid 3D structure(s).Nucleic acid property (structural)Molecular propertyA report on the physical (e.g. structural) or chemical properties of molecules, or parts of a molecule.Physicochemical propertySO:0000400beta12orEarlierDNA base structural dataStructural data for DNA base pairs or runs of bases, such as energy or angle data.beta12orEarlierDatabase entry version informationbeta12orEarliertrue1.5Information on a database (or ontology) entry version, such as name (or other identifier) or parent database, unique identifier of entry, data, author and so on.Accessionbeta12orEarlierhttp://semanticscience.org/resource/SIO_000731A persistent (stable) and unique identifier, typically identifying an object (entry) from a database.http://semanticscience.org/resource/SIO_000675SNPbeta12orEarliertrue1.8single nucleotide polymorphism (SNP) in a DNA sequence.Data referenceReference to a dataset (or a cross-reference between two datasets), typically one or more entries in a biological database or ontology.A list of database accessions or identifiers are usually included.beta12orEarlierJob identifierhttp://wsio.org/data_009beta12orEarlierAn identifier of a submitted job.NameSymbolic namehttp://semanticscience.org/resource/SIO_000116beta12orEarlier"http://www.w3.org/2000/01/rdf-schema#labelhttp://usefulinc.com/ns/doap#nameA name of a thing, which need not necessarily uniquely identify it.Closely related, but focusing on labeling and human readability but not on identification.Typehttp://purl.org/dc/elements/1.1/type1.5beta12orEarliertrueA label (text token) describing the type of a thing, typically an enumerated string (a string with one of a limited set of values).User IDbeta12orEarlierAn identifier of a software end-user (typically a person).KEGG organism codebeta12orEarlierA three-letter code used in the KEGG databases to uniquely identify organisms.Gene name (KEGG GENES)Moby_namespace:GeneId1.3beta12orEarliertrue[a-zA-Z_0-9]+:[a-zA-Z_0-9\.-]*Name of an entry (gene) from the KEGG GENES database.BioCyc IDbeta12orEarlierIdentifier of an object from one of the BioCyc databases.Compound ID (BioCyc)BioCyc compound identifierBioCyc compound IDIdentifier of a compound from the BioCyc chemical compounds database.beta12orEarlierReaction ID (BioCyc)Identifier of a biological reaction from the BioCyc reactions database.beta12orEarlierEnzyme ID (BioCyc)BioCyc enzyme IDIdentifier of an enzyme from the BioCyc enzymes database.beta12orEarlierReaction IDbeta12orEarlierIdentifier of a biological reaction from a database.Identifier (hybrid)This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'.An identifier that is re-used for data objects of fundamentally different types (typically served from a single database).beta12orEarlierMolecular property identifierbeta12orEarlierIdentifier of a molecular property.Codon usage table IDCodon usage table identifierIdentifier of a codon usage table, for example a genetic code.beta12orEarlierFlyBase primary identifierPrimary identifier of an object from the FlyBase database.beta12orEarlierWormBase identifierbeta12orEarlierIdentifier of an object from the WormBase database.WormBase wormpep IDCE[0-9]{5}beta12orEarlierProtein identifier used by WormBase database.Nucleic acid features (codon)An informative report on a trinucleotide sequence that encodes an amino acid including the triplet sequence, the encoded amino acid or whether it is a start or stop codon.beta12orEarliertruebeta12orEarlierMap identifierbeta12orEarlierAn identifier of a map of a molecular sequence.Person identifierAn identifier of a software end-user (typically a person).beta12orEarlierNucleic acid identifierbeta12orEarlierName or other identifier of a nucleic acid molecule.Translation frame specificationbeta12orEarlierFrame for translation of DNA (3 forward and 3 reverse frames relative to a chromosome).Genetic code identifierAn identifier of a genetic code.beta12orEarlierGenetic code nameInformal name for a genetic code, typically an organism name.beta12orEarlierFile format nameName of a file format such as HTML, PNG, PDF, EMBL, GenBank and so on.beta12orEarlierSequence profile typebeta12orEarliertrue1.5A label (text token) describing a type of sequence profile such as frequency matrix, Gribskov profile, hidden Markov model etc.Operating system namebeta12orEarlierName of a computer operating system such as Linux, PC or Mac.Mutation typeA type of point or block mutation, including insertion, deletion, change, duplication and moves.beta12orEarliertruebeta12orEarlierLogical operatorA logical operator such as OR, AND, XOR, and NOT.beta12orEarlierResults sort orderPossible options including sorting by score, rank, by increasing P-value (probability, i.e. most statistically significant hits given first) and so on.1.5beta12orEarliertrueA control of the order of data that is output, for example the order of sequences in an alignment.Toggletruebeta12orEarlierA simple parameter that is a toggle (boolean value), typically a control for a modal tool.beta12orEarlierSequence widthbeta12orEarlierThe width of an output sequence or alignment.truebeta12orEarlierGap penaltybeta12orEarlierA penalty for introducing or extending a gap in an alignment.Nucleic acid melting temperatureMelting temperaturebeta12orEarlierA temperature concerning nucleic acid denaturation, typically the temperature at which the two strands of a hybridised or double stranded nucleic acid (DNA or RNA/DNA) molecule separate.Concentrationbeta12orEarlierThe concentration of a chemical compound.Window step sizetrueSize of the incremental 'step' a sequence window is moved over a sequence.1.5beta12orEarlierEMBOSS graphbeta12orEarlierbeta12orEarliertrueAn image of a graph generated by the EMBOSS suite.EMBOSS reporttruebeta12orEarlierbeta12orEarlierAn application report generated by the EMBOSS suite.Sequence offset1.5trueAn offset for a single-point sequence position.beta12orEarlierThresholdtrueA value that serves as a threshold for a tool (usually to control scoring or output).1.5beta12orEarlierProtein report (transcription factor)This might include conformational or physicochemical properties, as well as sequence information for transcription factor(s) binding sites.beta12orEarlierbeta13trueAn informative report on a transcription factor protein.Database category namebeta12orEarlierbeta12orEarlierThe name of a category of biological or bioinformatics database.trueSequence profile nameName of a sequence profile.beta12orEarliertruebeta12orEarlierColorbeta12orEarlierSpecification of one or more colors.beta12orEarliertrueRendering parameterA parameter that is used to control rendering (drawing) to a device or image.1.5truebeta12orEarlierSequence nameAny arbitrary name of a molecular sequence.beta12orEarlierDate1.5beta12orEarliertrueA temporal date.Word compositionWord composition data for a molecular sequence.beta12orEarliertruebeta12orEarlierFickett testcode plotbeta12orEarlierA plot of Fickett testcode statistic (identifying protein coding regions) in a nucleotide sequences.Sequence similarity plotA plot of sequence similarities identified from word-matching or character comparison.Use this concept for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc.Sequence conservation reportbeta12orEarlierHelical wheelbeta12orEarlierAn image of peptide sequence sequence looking down the axis of the helix for highlighting amphipathicity and other properties.Helical netUseful for highlighting amphipathicity and other properties.An image of peptide sequence sequence in a simple 3,4,3,4 repeating pattern that emulates at a simple level the arrangement of residues around an alpha helix.beta12orEarlierProtein sequence properties plotbeta12orEarliertrueA plot of general physicochemical properties of a protein sequence.beta12orEarlierProtein ionisation curveA plot of pK versus pH for a protein.beta12orEarlierSequence composition plotbeta12orEarlierA plot of character or word composition / frequency of a molecular sequence.Nucleic acid density plotDensity plot (of base composition) for a nucleotide sequence.beta12orEarlierSequence trace imageImage of a sequence trace (nucleotide sequence versus probabilities of each of the 4 bases).beta12orEarlierNucleic acid features (siRNA)1.5A report on siRNA duplexes in mRNA.truebeta12orEarlierSequence set (stream)beta12orEarlierThis concept may be used for sequence sets that are expected to be read and processed a single sequence at a time.truebeta12orEarlierA collection of multiple molecular sequences and (typically) associated metadata that is intended for sequential processing.FlyBase secondary identifierSecondary identifier are used to handle entries that were merged with or split from other entries in the database.Secondary identifier of an object from the FlyBase database.beta12orEarlierCardinalityThe number of a certain thing.beta12orEarliertruebeta12orEarlierExactly 1truebeta12orEarlierbeta12orEarlierA single thing.1 or moretruebeta12orEarlierOne or more things.beta12orEarlierExactly 2beta12orEarlierbeta12orEarlierExactly two things.true2 or moretruebeta12orEarlierTwo or more things.beta12orEarlierSequence checksumHashbeta12orEarlierA fixed-size datum calculated (by using a hash function) for a molecular sequence, typically for purposes of error detection or indexing.Hash codeHash valueHash sumProtein features report (chemical modifications)1.8chemical modification of a protein.beta12orEarliertrueErrorbeta12orEarliertrue1.5Data on an error generated by computer system or tool.Database entry metadatabeta12orEarlierBasic information on any arbitrary database entry.Gene clusterA cluster of similar genes.truebeta12orEarlierbeta13Sequence record fullA molecular sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database.1.8beta12orEarliertruePlasmid identifierbeta12orEarlierAn identifier of a plasmid in a database.Mutation IDbeta12orEarlierA unique identifier of a specific mutation catalogued in a database.Mutation annotation (basic)Information describing the mutation itself, the organ site, tissue and type of lesion where the mutation has been identified, description of the patient origin and life-style.beta12orEarlierbeta12orEarliertrueMutation annotation (prevalence)beta12orEarlierbeta12orEarliertrueAn informative report on the prevalence of mutation(s), including data on samples and mutation prevalence (e.g. by tumour type)..Mutation annotation (prognostic)An informative report on mutation prognostic data, such as information on patient cohort, the study settings and the results of the study.beta12orEarlierbeta12orEarliertrueMutation annotation (functional)beta12orEarlierbeta12orEarliertrueAn informative report on the functional properties of mutant proteins including transcriptional activities, promotion of cell growth and tumorigenicity, dominant negative effects, capacity to induce apoptosis, cell-cycle arrest or checkpoints in human cells and so on.Codon numberbeta12orEarlierThe number of a codon, for instance, at which a mutation is located.Tumor annotationtruebeta12orEarlier1.4An informative report on a specific tumor including nature and origin of the sample, anatomic site, organ or tissue, tumor type, including morphology and/or histologic type, and so on.Server metadataBasic information about a server on the web, such as an SRS server.1.5beta12orEarliertrueDatabase field nameThe name of a field in a database.beta12orEarlierSequence cluster ID (SYSTERS)SYSTERS cluster IDbeta12orEarlierUnique identifier of a sequence cluster from the SYSTERS database.Ontology metadataData concerning a biological ontology.beta12orEarlierRaw SCOP domain classificationbeta12orEarlierRaw SCOP domain classification data files.truebeta13These are the parsable data files provided by SCOP.Raw CATH domain classificationRaw CATH domain classification data files.These are the parsable data files provided by CATH.beta13truebeta12orEarlierHeterogen annotationbeta12orEarlier1.4An informative report on the types of small molecules or 'heterogens' (non-protein groups) that are represented in PDB files.truePhylogenetic property valuesPhylogenetic property values data.truebeta12orEarlierbeta12orEarlierSequence set (bootstrapped)A collection of sequences output from a bootstrapping (resampling) procedure.Bootstrapping is often performed in phylogenetic analysis.beta12orEarliertrue1.5Phylogenetic consensus treeA consensus phylogenetic tree derived from comparison of multiple trees.beta12orEarliertruebeta12orEarlierSchematruebeta12orEarlier1.5A data schema for organising or transforming data of some type.DTD1.5A DTD (document type definition).beta12orEarliertrueXML Schematruebeta12orEarlier1.5An XML Schema.Relax-NG schematruebeta12orEarlier1.5A relax-NG schema.XSLT stylesheetAn XSLT stylesheet.beta12orEarliertrue1.5Data resource definition namebeta12orEarlierThe name of a data type.OBO file format namebeta12orEarlierName of an OBO file format such as OBO-XML, plain and so on.Gene ID (MIPS)Identifier for genetic elements in MIPS database.beta12orEarlierMIPS genetic element identifierSequence identifier (protein)An identifier of protein sequence(s) or protein sequence database entries.beta12orEarlierbeta12orEarliertrueSequence identifier (nucleic acid)An identifier of nucleotide sequence(s) or nucleotide sequence database entries.beta12orEarliertruebeta12orEarlierEMBL accessionEMBL identifierEMBL IDAn accession number of an entry from the EMBL sequence database.EMBL accession numberbeta12orEarlierUniProt IDUniProtKB entry nameUniProt identifierbeta12orEarlierUniProtKB identifierAn identifier of a polypeptide in the UniProt database.UniProt entry nameGenBank accessionbeta12orEarlierGenBank IDGenBank accession numberGenBank identifierAccession number of an entry from the GenBank sequence database.Gramene secondary identifierSecondary (internal) identifier of a Gramene database entry.Gramene internal identifierbeta12orEarlierGramene internal IDGramene secondary IDSequence variation IDbeta12orEarlierAn identifier of an entry from a database of molecular sequence variation.Gene IDA unique (and typically persistent) identifier of a gene in a database, that is (typically) different to the gene name/symbol.Gene accessionbeta12orEarlierGene codeGene name (AceView)beta12orEarliertrueName of an entry (gene) from the AceView genes database.1.3Gene ID (ECK)E. coli K-12 gene identifierECK accessionhttp://www.geneontology.org/doc/GO.xrf_abbs: ECKbeta12orEarlierIdentifier of an E. coli K-12 gene from EcoGene Database.Gene ID (HGNC)Identifier for a gene approved by the HUGO Gene Nomenclature Committee.HGNC IDbeta12orEarlierGene nameThe name of a gene, (typically) assigned by a person and/or according to a naming scheme. It may contain white space characters and is typically more intuitive and readable than a gene symbol. It (typically) may be used to identify similar genes in different species and to derive a gene symbol.Allele namebeta12orEarlierGene name (NCBI)Name of an entry (gene) from the NCBI genes database.beta12orEarliertrueNCBI gene name1.3SMILES stringA specification of a chemical structure in SMILES format.beta12orEarlierSTRING IDUnique identifier of an entry from the STRING database of protein-protein interactions.beta12orEarlierVirus annotationAn informative report on a specific virus.beta12orEarliertrue1.4Virus annotation (taxonomy)1.4truebeta12orEarlierAn informative report on the taxonomy of a specific virus.Reaction ID (SABIO-RK)Identifier of a biological reaction from the SABIO-RK reactions database.[0-9]+beta12orEarlierCarbohydrate reportAnnotation on or information derived from one or more specific carbohydrate 3D structure(s).beta12orEarlierGI numberbeta12orEarliergi numberA series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Accession number of the sequence record.NCBI GI numberNucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record.NCBI versionNCBI accession.versionNucleotide sequence version contains two letters followed by six digits, a dot, and a version number (or for older nucleotide sequence records, the format is one letter followed by five digits, a dot, and a version number). Protein sequence version contains three letters followed by five digits, a dot, and a version number.An identifier assigned to sequence records processed by NCBI, made of the accession number of the database record followed by a dot and a version number.accession.versionbeta12orEarlierCell line namebeta12orEarlierThe name of a cell line.Cell line name (exact)The name of a cell line.beta12orEarlierCell line name (truncated)The name of a cell line.beta12orEarlierCell line name (no punctuation)beta12orEarlierThe name of a cell line.Cell line name (assonant)beta12orEarlierThe name of a cell line.Enzyme IDA unique, persistent identifier of an enzyme.Enzyme accessionbeta12orEarlierREBASE enzyme numberbeta12orEarlierIdentifier of an enzyme from the REBASE enzymes database.DrugBank IDUnique identifier of a drug from the DrugBank database.beta12orEarlierDB[0-9]{5}GI number (protein)A unique identifier assigned to NCBI protein sequence records.protein gi numberbeta12orEarlierNucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record.protein giBit scoreA score derived from the alignment of two sequences, which is then normalised with respect to the scoring system.beta12orEarlierBit scores are normalised with respect to the scoring system and therefore can be used to compare alignment scores from different searches.Translation phase specificationbeta12orEarlierPhasePhase for translation of DNA (0, 1 or 2) relative to a fragment of the coding sequence.Resource metadataData concerning or describing some core computational resource, as distinct from primary data. This includes metadata on the origin, source, history, ownership or location of some thing.Provenance metadatabeta12orEarlierThis is a broad data type and is used a placeholder for other, more specific types.Ontology identifierbeta12orEarlierAny arbitrary identifier of an ontology.Ontology concept nameThe name of a concept in an ontology.beta12orEarlierGenome build identifierAn identifier of a build of a particular genome.beta12orEarlierPathway or network nameThe name of a biological pathway or network.beta12orEarlierPathway ID (KEGG)beta12orEarlierIdentifier of a pathway from the KEGG pathway database.KEGG pathway ID[a-zA-Z_0-9]{2,3}[0-9]{5}Pathway ID (NCI-Nature)beta12orEarlier[a-zA-Z_0-9]+Identifier of a pathway from the NCI-Nature pathway database.Pathway ID (ConsensusPathDB)Identifier of a pathway from the ConsensusPathDB pathway database.beta12orEarlierSequence cluster ID (UniRef)UniRef entry accessionUnique identifier of an entry from the UniRef database.beta12orEarlierUniRef cluster idSequence cluster ID (UniRef100)UniRef100 cluster idUnique identifier of an entry from the UniRef100 database.UniRef100 entry accessionbeta12orEarlierSequence cluster ID (UniRef90)beta12orEarlierUniRef90 entry accessionUnique identifier of an entry from the UniRef90 database.UniRef90 cluster idSequence cluster ID (UniRef50)Unique identifier of an entry from the UniRef50 database.beta12orEarlierUniRef50 entry accessionUniRef50 cluster idOntology dataData concerning or derived from an ontology.This is a broad data type and is used a placeholder for other, more specific types.beta12orEarlierOntological dataRNA family reportAn informative report on a specific RNA family or other group of classified RNA sequences.beta12orEarlierRNA family annotationRNA family identifierbeta12orEarlierIdentifier of an RNA family, typically an entry from a RNA sequence classification database.RFAM accessionStable accession number of an entry (RNA family) from the RFAM database.beta12orEarlierProtein signature type1.5truebeta12orEarlierA label (text token) describing a type of protein family signature (sequence classifier) from the InterPro database.Domain-nucleic acid interaction reportAn informative report on protein domain-DNA/RNA interaction(s).1.5truebeta12orEarlierDomain-domain interactionsbeta12orEarliertrueAn informative report on protein domain-protein domain interaction(s).1.8Domain-domain interaction (indirect)Data on indirect protein domain-protein domain interaction(s).beta12orEarliertruebeta12orEarlierSequence accession (hybrid)beta12orEarlierAccession number of a nucleotide or protein sequence database entry.2D PAGE dataData concerning two-dimensional polygel electrophoresis.beta12orEarliertruebeta13This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.2D PAGE report1.8two-dimensional gel electrophoresis experiments, gels or spots in a gel.truebeta12orEarlierPathway or network accessionbeta12orEarlierA persistent, unique identifier of a biological pathway or network (typically a database entry).Secondary structure alignmentAlignment of the (1D representations of) secondary structure of two or more molecules.beta12orEarlierASTD IDIdentifier of an object from the ASTD database.beta12orEarlierASTD ID (exon)beta12orEarlierIdentifier of an exon from the ASTD database.ASTD ID (intron)Identifier of an intron from the ASTD database.beta12orEarlierASTD ID (polya)beta12orEarlierIdentifier of a polyA signal from the ASTD database.ASTD ID (tss)Identifier of a transcription start site from the ASTD database.beta12orEarlier2D PAGE spot reporttruebeta12orEarlierAn informative report on individual spot(s) from a two-dimensional (2D PAGE) gel.1.8Spot IDUnique identifier of a spot from a two-dimensional (protein) gel.beta12orEarlierSpot serial numberbeta12orEarlierUnique identifier of a spot from a two-dimensional (protein) gel in the SWISS-2DPAGE database.Spot ID (HSC-2DPAGE)Unique identifier of a spot from a two-dimensional (protein) gel from a HSC-2DPAGE database.beta12orEarlierProtein-motif interactionbeta13Data on the interaction of a protein (or protein domain) with specific structural (3D) and/or sequence motifs.truebeta12orEarlierStrain identifierbeta12orEarlierIdentifier of a strain of an organism variant, typically a plant, virus or bacterium.CABRI accessionA unique identifier of an item from the CABRI database.beta12orEarlierExperiment report (genotyping)Report of genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods.beta12orEarliertrue1.8Genotype experiment IDIdentifier of an entry from a database of genotype experiment metadata.beta12orEarlierEGA accessionIdentifier of an entry from the EGA database.beta12orEarlierIPI protein IDIPI[0-9]{8}Identifier of a protein entry catalogued in the International Protein Index (IPI) database.beta12orEarlierRefSeq accession (protein)beta12orEarlierAccession number of a protein from the RefSeq database.RefSeq protein IDEPD IDIdentifier of an entry (promoter) from the EPD database.beta12orEarlierEPD identifierTAIR accessionbeta12orEarlierIdentifier of an entry from the TAIR database.TAIR accession (At gene)beta12orEarlierIdentifier of an Arabidopsis thaliana gene from the TAIR database.UniSTS accessionIdentifier of an entry from the UniSTS database.beta12orEarlierUNITE accessionIdentifier of an entry from the UNITE database.beta12orEarlierUTR accessionIdentifier of an entry from the UTR database.beta12orEarlierUniParc accessionUPIbeta12orEarlierUniParc IDAccession number of a UniParc (protein sequence) database entry.UPI[A-F0-9]{10}mFLJ/mKIAA numberIdentifier of an entry from the Rouge or HUGE databases.beta12orEarlierFungi annotationAn informative report on a specific fungus.truebeta12orEarlier1.4Fungi annotation (anamorph)beta12orEarliertrueAn informative report on a specific fungus anamorph.1.4Gene features report (exon)exons in a nucleotide sequences.1.8beta12orEarliertrueEnsembl protein IDbeta12orEarlierUnique identifier for a protein from the Ensembl database.Protein ID (Ensembl)Ensembl ID (protein)Gene transcriptional features report1.8truebeta12orEarliertranscription of DNA into RNA including the regulation of transcription.Toxin annotationAn informative report on a specific toxin.1.4beta12orEarliertrueProtein report (membrane protein)beta12orEarlierbeta12orEarliertrueAn informative report on a membrane protein.Protein-drug interaction report1.12An informative report on tentative or known protein-drug interaction(s).truebeta12orEarlierMap databeta13beta12orEarliertrueThis is a broad data type and is used a placeholder for other, more specific types.Data concerning a map of molecular sequence(s).Phylogenetic dataThis is a broad data type and is used a placeholder for other, more specific types.Data concerning phylogeny, typically of molecular sequences, including reports of information concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees.beta12orEarlierProtein databeta13beta12orEarliertrueThis is a broad data type and is used a placeholder for other, more specific types.Data concerning one or more protein molecules.Nucleic acid dataData concerning one or more nucleic acid molecules.beta13truebeta12orEarlierThis is a broad data type and is used a placeholder for other, more specific types.Text databeta12orEarlierArticle dataScientific text dataThis is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. It includes concepts that are best described as scientific text or closely concerned with or derived from text.Data concerning, extracted from, or derived from the analysis of a scientific text (or texts) such as a full text article from a scientific journal.Parameter1.16Typically a simple numerical or string value that controls the operation of a tool.truebeta12orEarlierMolecular dataThis is a broad data type and is used a placeholder for other, more specific types.Data concerning a specific type of molecule.beta13beta12orEarliertrueMolecule reporttruebeta12orEarlier1.5An informative report on a specific molecule.Organism reportOrganism annotationbeta12orEarlierAn informative report on a specific organism.Experiment reportbeta12orEarlierExperiment metadataAnnotation on a wet lab experiment, such as experimental conditions.Experiment annotationNucleic acid features report (mutation)truebeta12orEarlier1.8DNA mutation.Sequence attributeSequence parameterAn attribute of a molecular sequence, possibly in reference to some other sequence.beta12orEarlierSequence tag profileSequence tag profile (with gene assignment)beta12orEarlierSAGE, MPSS and SBS experiments are usually performed to study gene expression. The sequence tags are typically subsequently annotated (after a database search) with the mRNA (and therefore gene) the tag was extracted from.This includes tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data. Typically this is the sequencing-based expression profile annotated with gene identifiers.Output from a serial analysis of gene expression (SAGE), massively parallel signature sequencing (MPSS) or sequencing by synthesis (SBS) experiment. In all cases this is a list of short sequence tags and the number of times it is observed.Sequencing-based expression profileMass spectrometry databeta12orEarlierData concerning a mass spectrometry measurement.Protein structure raw dataThis is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.beta12orEarlierRaw data from experimental methods for determining protein structure.Mutation identifierAn identifier of a mutation.beta12orEarlierAlignment dataThis is a broad data type and is used a placeholder for other, more specific types. This includes entities derived from sequences and structures such as motifs and profiles.beta12orEarliertruebeta13Data concerning an alignment of two or more molecular sequences, structures or derived data.Data index databeta12orEarliertruebeta13Data concerning an index of data.This is a broad data type and is used a placeholder for other, more specific types.Amino acid name (single letter)beta12orEarlierSingle letter amino acid identifier, e.g. G.Amino acid name (three letter)Three letter amino acid identifier, e.g. GLY.beta12orEarlierAmino acid name (full name)Full name of an amino acid, e.g. Glycine.beta12orEarlierToxin identifierIdentifier of a toxin.beta12orEarlierArachnoServer IDbeta12orEarlierUnique identifier of a toxin from the ArachnoServer database.Expressed gene list1.5A simple summary of expressed genes.beta12orEarliertrueBindingDB Monomer IDbeta12orEarlierUnique identifier of a monomer from the BindingDB database.GO concept nameThe name of a concept from the GO ontology.beta12orEarliertruebeta12orEarlierGO concept ID (biological process)beta12orEarlierAn identifier of a 'biological process' concept from the the Gene Ontology.[0-9]{7}|GO:[0-9]{7}GO concept ID (molecular function)[0-9]{7}|GO:[0-9]{7}beta12orEarlierAn identifier of a 'molecular function' concept from the the Gene Ontology.GO concept name (cellular component)beta12orEarliertruebeta12orEarlierThe name of a concept for a cellular component from the GO ontology.Northern blot imageAn image arising from a Northern Blot experiment.beta12orEarlierBlot IDUnique identifier of a blot from a Northern Blot.beta12orEarlierBlotBase blot IDUnique identifier of a blot from a Northern Blot from the BlotBase database.beta12orEarlierHierarchyRaw data on a biological hierarchy, describing the hierarchy proper, hierarchy components and possibly associated annotation.beta12orEarlierHierarchy annotationHierarchy identifierIdentifier of an entry from a database of biological hierarchies.beta12orEarliertruebeta12orEarlierBrite hierarchy IDIdentifier of an entry from the Brite database of biological hierarchies.beta12orEarlierCancer typeA type (represented as a string) of cancer.beta12orEarliertruebeta12orEarlierBRENDA organism IDbeta12orEarlierA unique identifier for an organism used in the BRENDA database.UniGene taxonThe name of a taxon using the controlled vocabulary of the UniGene database.UniGene organism abbreviationbeta12orEarlierUTRdb taxonbeta12orEarlierThe name of a taxon using the controlled vocabulary of the UTRdb database.Catalogue IDCatalogue identifierAn identifier of a catalogue of biological resources.beta12orEarlierCABRI catalogue nameThe name of a catalogue of biological resources from the CABRI database.beta12orEarlierSecondary structure alignment metadatabeta12orEarlierbeta12orEarliertrueAn informative report on protein secondary structure alignment-derived data or metadata.Molecule interaction reportAn informative report on the physical, chemical or other information concerning the interaction of two or more molecules (or parts of molecules).beta12orEarlierPathway or networkPathwaybeta12orEarlierPrimary data about a specific biological pathway or network (the nodes and connections within the pathway or network).NetworkSmall molecule dataData concerning one or more small molecules.This is a broad data type and is used a placeholder for other, more specific types.beta12orEarliertruebeta13Genotype and phenotype databeta12orEarliertruebeta13Data concerning a particular genotype, phenotype or a genotype / phenotype relation.Microarray dataGene expression dataRNA quantification dataProtein quantification dataProtein profileTranscriptome quantification dataMicroarray dataGene product quantification dataImage, hybridisation or some other data arising from a study of gene expression, typically profiling or quantification.Transcriptome profileRNA-seq dataGene transcription profileProteome quantification dataNon-coding RNA quantification dataRNA profilebeta12orEarlierGene product profilemRNA quantification datamRNA profileProteome profileNon-coding RNA profileGene transcription quantification dataCompound ID (KEGG)C[0-9]+Unique identifier of a chemical compound from the KEGG database.beta12orEarlierKEGG compound identifierKEGG compound IDRFAM nameName (not necessarily stable) an entry (RNA family) from the RFAM database.beta12orEarlierReaction ID (KEGG)Identifier of a biological reaction from the KEGG reactions database.R[0-9]+beta12orEarlierDrug ID (KEGG)D[0-9]+Unique identifier of a drug from the KEGG Drug database.beta12orEarlierEnsembl IDENS[A-Z]*[FPTG][0-9]{11}Identifier of an entry (exon, gene, transcript or protein) from the Ensembl database.Ensembl IDsbeta12orEarlierICD identifier[A-Z][0-9]+(\.[-[0-9]+])?beta12orEarlierAn identifier of a disease from the International Classification of Diseases (ICD) database.Sequence cluster ID (CluSTr)CluSTr IDUnique identifier of a sequence cluster from the CluSTr database.beta12orEarlierCluSTr cluster ID[0-9A-Za-z]+:[0-9]+:[0-9]{1,5}(\.[0-9])?KEGG Glycan IDbeta12orEarlierUnique identifier of a glycan ligand from the KEGG GLYCAN database (a subset of KEGG LIGAND).G[0-9]+TCDB IDA unique identifier of a family from the transport classification database (TCDB) of membrane transport proteins.[0-9]+\.[A-Z]\.[0-9]+\.[0-9]+\.[0-9]+OBO file for regular expression.beta12orEarlierTC numberMINT IDbeta12orEarlierUnique identifier of an entry from the MINT database of protein-protein interactions.MINT\-[0-9]{1,5}DIP IDbeta12orEarlierDIP[\:\-][0-9]{3}[EN]Unique identifier of an entry from the DIP database of protein-protein interactions.Signaling Gateway protein IDA[0-9]{6}Unique identifier of a protein listed in the UCSD-Nature Signaling Gateway Molecule Pages database.beta12orEarlierProtein modification IDbeta12orEarlierIdentifier of a protein modification catalogued in a database.RESID IDIdentifier of a protein modification catalogued in the RESID database.AA[0-9]{4}beta12orEarlierRGD IDbeta12orEarlier[0-9]{4,7}Identifier of an entry from the RGD database.TAIR accession (protein)Identifier of a protein sequence from the TAIR database.AASequence:[0-9]{10}beta12orEarlierCompound ID (HMDB)Identifier of a small molecule metabolite from the Human Metabolome Database (HMDB).beta12orEarlierHMDB IDHMDB[0-9]{5}LIPID MAPS IDIdentifier of an entry from the LIPID MAPS database.beta12orEarlierLM IDLM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4})?PeptideAtlas IDIdentifier of a peptide from the PeptideAtlas peptide databases.beta12orEarlierPAp[0-9]{8}PDBML:pdbx_PDB_strand_idMolecular interaction ID1.7truebeta12orEarlierIdentifier of a report of molecular interactions from a database (typically).BioGRID interaction IDA unique identifier of an interaction from the BioGRID database.[0-9]+beta12orEarlierEnzyme ID (MEROPS)Unique identifier of a peptidase enzyme from the MEROPS database.S[0-9]{2}\.[0-9]{3}MEROPS IDbeta12orEarlierMobile genetic element IDbeta12orEarlierAn identifier of a mobile genetic element.ACLAME IDmge:[0-9]+beta12orEarlierAn identifier of a mobile genetic element from the Aclame database.SGD IDPWY[a-zA-Z_0-9]{2}\-[0-9]{3}Identifier of an entry from the Saccharomyces genome database (SGD).beta12orEarlierBook IDUnique identifier of a book.beta12orEarlierISBNThe International Standard Book Number (ISBN) is for identifying printed books.beta12orEarlier(ISBN)?(-13|-10)?[:]?[ ]?([0-9]{2,3}[ -]?)?[0-9]{1,5}[ -]?[0-9]{1,7}[ -]?[0-9]{1,6}[ -]?([0-9]|X)Compound ID (3DMET)beta12orEarlierIdentifier of a metabolite from the 3DMET database.3DMET IDB[0-9]{5}MatrixDB interaction IDbeta12orEarlierA unique identifier of an interaction from the MatrixDB database.([A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9])_.*|([OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)cPath IDbeta12orEarlierA unique identifier for pathways, reactions, complexes and small molecules from the cPath (Pathway Commons) database.[0-9]+These identifiers are unique within the cPath database, however, they are not stable between releases.PubChem bioassay ID[0-9]+beta12orEarlierIdentifier of an assay from the PubChem database.PubChem IDPubChem identifierbeta12orEarlierIdentifier of an entry from the PubChem database.Reaction ID (MACie)Identifier of an enzyme reaction mechanism from the MACie database.MACie entry numberbeta12orEarlierM[0-9]{4}Gene ID (miRBase)beta12orEarliermiRNA namemiRNA IDmiRNA identifierIdentifier for a gene from the miRBase database.MI[0-9]{7}Gene ID (ZFIN)ZDB\-GENE\-[0-9]+\-[0-9]+beta12orEarlierIdentifier for a gene from the Zebrafish information network genome (ZFIN) database.Reaction ID (Rhea)beta12orEarlierIdentifier of an enzyme-catalysed reaction from the Rhea database.[0-9]{5}Pathway ID (Unipathway)Identifier of a biological pathway from the Unipathway database.UPA[0-9]{5}upaidbeta12orEarlierCompound ID (ChEMBL)ChEMBL IDbeta12orEarlier[0-9]+Identifier of a small molecular from the ChEMBL database.LGICdb identifier[a-zA-Z_0-9]+Unique identifier of an entry from the Ligand-gated ion channel (LGICdb) database.beta12orEarlierReaction kinetics ID (SABIO-RK)beta12orEarlierIdentifier of a biological reaction (kinetics entry) from the SABIO-RK reactions database.[0-9]+PharmGKB IDbeta12orEarlierIdentifier of an entry from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).PA[0-9]+Pathway ID (PharmGKB)Identifier of a pathway from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).beta12orEarlierPA[0-9]+Disease ID (PharmGKB)Identifier of a disease from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).beta12orEarlierPA[0-9]+Drug ID (PharmGKB)PA[0-9]+beta12orEarlierIdentifier of a drug from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).Drug ID (TTD)beta12orEarlierIdentifier of a drug from the Therapeutic Target Database (TTD).DAP[0-9]+Target ID (TTD)Identifier of a target protein from the Therapeutic Target Database (TTD).TTDS[0-9]+beta12orEarlierCell type identifierA unique identifier of a type or group of cells.beta12orEarlierNeuronDB ID[0-9]+A unique identifier of a neuron from the NeuronDB database.beta12orEarlierNeuroMorpho ID[a-zA-Z_0-9]+beta12orEarlierA unique identifier of a neuron from the NeuroMorpho database.Compound ID (ChemIDplus)Identifier of a chemical from the ChemIDplus database.ChemIDplus IDbeta12orEarlier[0-9]+Pathway ID (SMPDB)Identifier of a pathway from the Small Molecule Pathway Database (SMPDB).beta12orEarlierSMP[0-9]{5}BioNumbers ID[0-9]+Identifier of an entry from the BioNumbers database of key numbers and associated data in molecular biology.beta12orEarlierT3DB IDT3D[0-9]+Unique identifier of a toxin from the Toxin and Toxin Target Database (T3DB) database.beta12orEarlierCarbohydrate identifierIdentifier of a carbohydrate.beta12orEarlierGlycomeDB IDbeta12orEarlierIdentifier of an entry from the GlycomeDB database.[0-9]+LipidBank IDIdentifier of an entry from the LipidBank database.beta12orEarlier[a-zA-Z_0-9]+[0-9]+CDD IDcd[0-9]{5}beta12orEarlierIdentifier of a conserved domain from the Conserved Domain Database.MMDB IDAn identifier of an entry from the MMDB database.MMDB accession[0-9]{1,5}beta12orEarlieriRefIndex IDbeta12orEarlier[0-9]+Unique identifier of an entry from the iRefIndex database of protein-protein interactions.ModelDB IDUnique identifier of an entry from the ModelDB database.beta12orEarlier[0-9]+Pathway ID (DQCS)beta12orEarlier[0-9]+Identifier of a signaling pathway from the Database of Quantitative Cellular Signaling (DQCS).Ensembl ID (Homo sapiens)ENS([EGTP])[0-9]{11}beta12orEarlierIdentifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database (Homo sapiens division).beta12orEarliertrueEnsembl ID ('Bos taurus')beta12orEarlierIdentifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Bos taurus' division).truebeta12orEarlierENSBTA([EGTP])[0-9]{11}Ensembl ID ('Canis familiaris')ENSCAF([EGTP])[0-9]{11}beta12orEarlierIdentifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Canis familiaris' division).beta12orEarliertrueEnsembl ID ('Cavia porcellus')beta12orEarlierIdentifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Cavia porcellus' division).truebeta12orEarlierENSCPO([EGTP])[0-9]{11}Ensembl ID ('Ciona intestinalis')truebeta12orEarlierIdentifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona intestinalis' division).ENSCIN([EGTP])[0-9]{11}beta12orEarlierEnsembl ID ('Ciona savignyi')beta12orEarliertruebeta12orEarlierIdentifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona savignyi' division).ENSCSAV([EGTP])[0-9]{11}Ensembl ID ('Danio rerio')ENSDAR([EGTP])[0-9]{11}beta12orEarliertrueIdentifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Danio rerio' division).beta12orEarlierEnsembl ID ('Dasypus novemcinctus')beta12orEarlierIdentifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Dasypus novemcinctus' division).truebeta12orEarlierENSDNO([EGTP])[0-9]{11}Ensembl ID ('Echinops telfairi')ENSETE([EGTP])[0-9]{11}truebeta12orEarlierIdentifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Echinops telfairi' division).beta12orEarlierEnsembl ID ('Erinaceus europaeus')Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Erinaceus europaeus' division).beta12orEarliertruebeta12orEarlierENSEEU([EGTP])[0-9]{11}Ensembl ID ('Felis catus')Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Felis catus' division).truebeta12orEarlierbeta12orEarlierENSFCA([EGTP])[0-9]{11}Ensembl ID ('Gallus gallus')beta12orEarlierIdentifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gallus gallus' division).ENSGAL([EGTP])[0-9]{11}truebeta12orEarlierEnsembl ID ('Gasterosteus aculeatus')beta12orEarliertrueENSGAC([EGTP])[0-9]{11}Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gasterosteus aculeatus' division).beta12orEarlierEnsembl ID ('Homo sapiens')beta12orEarlierENSHUM([EGTP])[0-9]{11}Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Homo sapiens' division).truebeta12orEarlierEnsembl ID ('Loxodonta africana')ENSLAF([EGTP])[0-9]{11}beta12orEarlierbeta12orEarliertrueIdentifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Loxodonta africana' division).Ensembl ID ('Macaca mulatta')truebeta12orEarlierIdentifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Macaca mulatta' division).ENSMMU([EGTP])[0-9]{11}beta12orEarlierEnsembl ID ('Monodelphis domestica')ENSMOD([EGTP])[0-9]{11}beta12orEarlierIdentifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Monodelphis domestica' division).beta12orEarliertrueEnsembl ID ('Mus musculus')truebeta12orEarlierIdentifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Mus musculus' division).ENSMUS([EGTP])[0-9]{11}beta12orEarlierEnsembl ID ('Myotis lucifugus')ENSMLU([EGTP])[0-9]{11}beta12orEarlierIdentifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Myotis lucifugus' division).beta12orEarliertrueEnsembl ID ("Ornithorhynchus anatinus")beta12orEarliertrueIdentifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ornithorhynchus anatinus' division).ENSOAN([EGTP])[0-9]{11}beta12orEarlierEnsembl ID ('Oryctolagus cuniculus')ENSOCU([EGTP])[0-9]{11}beta12orEarliertruebeta12orEarlierIdentifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryctolagus cuniculus' division).Ensembl ID ('Oryzias latipes')beta12orEarliertruebeta12orEarlierIdentifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryzias latipes' division).ENSORL([EGTP])[0-9]{11}Ensembl ID ('Otolemur garnettii')beta12orEarlierENSSAR([EGTP])[0-9]{11}truebeta12orEarlierIdentifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Otolemur garnettii' division).Ensembl ID ('Pan troglodytes')Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Pan troglodytes' division).ENSPTR([EGTP])[0-9]{11}beta12orEarliertruebeta12orEarlierEnsembl ID ('Rattus norvegicus')beta12orEarlierENSRNO([EGTP])[0-9]{11}Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Rattus norvegicus' division).truebeta12orEarlierEnsembl ID ('Spermophilus tridecemlineatus')beta12orEarlierIdentifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Spermophilus tridecemlineatus' division).beta12orEarliertrueENSSTO([EGTP])[0-9]{11}Ensembl ID ('Takifugu rubripes')truebeta12orEarlierENSFRU([EGTP])[0-9]{11}Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Takifugu rubripes' division).beta12orEarlierEnsembl ID ('Tupaia belangeri')Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Tupaia belangeri' division).beta12orEarlierbeta12orEarliertrueENSTBE([EGTP])[0-9]{11}Ensembl ID ('Xenopus tropicalis')beta12orEarlierENSXET([EGTP])[0-9]{11}trueIdentifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Xenopus tropicalis' division).beta12orEarlierCATH identifierIdentifier of a protein domain (or other node) from the CATH database.beta12orEarlierCATH node ID (family)2.10.10.10beta12orEarlierA code number identifying a family from the CATH database.Enzyme ID (CAZy)CAZy IDIdentifier of an enzyme from the CAZy enzymes database.beta12orEarlierClone ID (IMAGE)A unique identifier assigned by the I.M.A.G.E. consortium to a clone (cloned molecular sequence).beta12orEarlierI.M.A.G.E. cloneIDIMAGE cloneIDGO concept ID (cellular component)An identifier of a 'cellular component' concept from the Gene Ontology.GO concept identifier (cellular compartment)beta12orEarlier[0-9]{7}|GO:[0-9]{7}Chromosome name (BioCyc)beta12orEarlierName of a chromosome as used in the BioCyc database.CleanEx entry namebeta12orEarlierAn identifier of a gene expression profile from the CleanEx database.CleanEx dataset codebeta12orEarlierAn identifier of (typically a list of) gene expression experiments catalogued in the CleanEx database.Genome reportAn informative report of general information concerning a genome as a whole.beta12orEarlierProtein ID (CORUM)CORUM complex IDUnique identifier for a protein complex from the CORUM database.beta12orEarlierCDD PSSM-IDbeta12orEarlierUnique identifier of a position-specific scoring matrix from the CDD database.Protein ID (CuticleDB)CuticleDB IDbeta12orEarlierUnique identifier for a protein from the CuticleDB database.DBD IDIdentifier of a predicted transcription factor from the DBD database.beta12orEarlierOligonucleotide probe annotationOligonucleotide probe sets annotationbeta12orEarlierGeneral annotation on an oligonucleotide probe, or a set of probes.Oligonucleotide IDbeta12orEarlierIdentifier of an oligonucleotide from a database.dbProbe IDbeta12orEarlierIdentifier of an oligonucleotide probe from the dbProbe database.Dinucleotide propertyPhysicochemical property data for one or more dinucleotides.beta12orEarlierDiProDB IDbeta12orEarlierIdentifier of an dinucleotide property from the DiProDB database.Protein features report (disordered structure)1.8disordered structure in a protein.beta12orEarliertrueProtein ID (DisProt)beta12orEarlierDisProt IDUnique identifier for a protein from the DisProt database.Embryo report1.5Annotation on an embryo or concerning embryological development.truebeta12orEarlierEnsembl transcript IDbeta12orEarlierUnique identifier for a gene transcript from the Ensembl database.Transcript ID (Ensembl)Inhibitor annotationtruebeta12orEarlierAn informative report on one or more small molecules that are enzyme inhibitors.1.4Promoter IDAn identifier of a promoter of a gene that is catalogued in a database.Moby:GeneAccessionListbeta12orEarlierEST accessionbeta12orEarlierIdentifier of an EST sequence.COGEME EST IDIdentifier of an EST sequence from the COGEME database.beta12orEarlierCOGEME unisequence IDbeta12orEarlierA unisequence is a single sequence assembled from ESTs.Identifier of a unisequence from the COGEME database.Protein family ID (GeneFarm)beta12orEarlierAccession number of an entry (family) from the TIGRFam database.GeneFarm family IDFamily namebeta12orEarlierThe name of a family of organism.Genus name (virus)beta13The name of a genus of viruses.beta12orEarliertrueFamily name (virus)truebeta12orEarlierbeta13The name of a family of viruses.Database name (SwissRegulon)beta13The name of a SwissRegulon database.beta12orEarliertrueSequence feature ID (SwissRegulon)This can be name of a gene, the ID of a TFBS, or genomic coordinates in form "chr:start..end".A feature identifier as used in the SwissRegulon database.beta12orEarlierFIG IDbeta12orEarlierA unique identifier of gene in the NMPDR database.A FIG ID consists of four parts: a prefix, genome id, locus type and id number.Gene ID (Xenbase)A unique identifier of gene in the Xenbase database.beta12orEarlierGene ID (Genolist)beta12orEarlierA unique identifier of gene in the Genolist database.Gene name (Genolist)Genolist gene name1.3Name of an entry (gene) from the Genolist genes database.beta12orEarliertrueABS IDIdentifier of an entry (promoter) from the ABS database.ABS identifierbeta12orEarlierAraC-XylS IDbeta12orEarlierIdentifier of a transcription factor from the AraC-XylS database.Gene name (HUGO)Name of an entry (gene) from the HUGO database.truebeta12orEarlierbeta12orEarlierLocus ID (PseudoCAP)Identifier of a locus from the PseudoCAP database.beta12orEarlierLocus ID (UTR)Identifier of a locus from the UTR database.beta12orEarlierMonosaccharideDB IDbeta12orEarlierUnique identifier of a monosaccharide from the MonosaccharideDB database.Database name (CMD)The name of a subdivision of the Collagen Mutation Database (CMD) database.truebeta12orEarlierbeta13Database name (Osteogenesis)beta13The name of a subdivision of the Osteogenesis database.beta12orEarliertrueGenome identifierAn identifier of a particular genome.beta12orEarlierGenomeReviews IDbeta12orEarlierAn identifier of a particular genome.GlycoMap IDIdentifier of an entry from the GlycosciencesDB database.[0-9]+beta12orEarlierCarbohydrate conformational mapbeta12orEarlierA conformational energy map of the glycosidic linkages in a carbohydrate molecule.Gene features report (intron)1.8introns in a nucleotide sequences.truebeta12orEarlierTranscription factor namebeta12orEarlierThe name of a transcription factor.TCIDbeta12orEarlierIdentifier of a membrane transport proteins from the transport classification database (TCDB).Pfam domain namebeta12orEarlierPF[0-9]{5}Name of a domain from the Pfam database.Pfam clan IDbeta12orEarlierAccession number of a Pfam clan.CL[0-9]{4}Gene ID (VectorBase)Identifier for a gene from the VectorBase database.beta12orEarlierVectorBase IDUTRSite IDIdentifier of an entry from the UTRSite database of regulatory motifs in eukaryotic UTRs.beta12orEarlierSequence signature reportSequence motif reportbeta12orEarlierAn informative report about a specific or conserved pattern in a molecular sequence, such as its context in genes or proteins, its role, origin or method of construction, etc.Sequence profile reportLocus annotationAn informative report on a particular locus.Locus reportbeta12orEarliertruebeta12orEarlierProtein name (UniProt)beta12orEarlierOfficial name of a protein as used in the UniProt database.Term ID listOne or more terms from one or more controlled vocabularies which are annotations on an entity.1.5truebeta12orEarlierThe concepts are typically provided as a persistent identifier or some other link the source ontologies. Evidence of the validity of the annotation might be included.HAMAP IDbeta12orEarlierName of a protein family from the HAMAP database.Identifier with metadata1.12Basic information concerning an identifier of data (typically including the identifier itself). For example, a gene symbol with information concerning its provenance.truebeta12orEarlierGene symbol annotationtruebeta12orEarlierbeta12orEarlierAnnotation about a gene symbol.Transcript IDIdentifier of a RNA transcript.beta12orEarlierHIT IDIdentifier of an RNA transcript from the H-InvDB database.beta12orEarlierHIX IDbeta12orEarlierA unique identifier of gene cluster in the H-InvDB database.HPA antibody idIdentifier of a antibody from the HPA database.beta12orEarlierIMGT/HLA IDbeta12orEarlierIdentifier of a human major histocompatibility complex (HLA) or other protein from the IMGT/HLA database.Gene ID (JCVI)beta12orEarlierA unique identifier of gene assigned by the J. Craig Venter Institute (JCVI).Kinase nameThe name of a kinase protein.beta12orEarlierConsensusPathDB entity IDIdentifier of a physical entity from the ConsensusPathDB database.beta12orEarlierConsensusPathDB entity namebeta12orEarlierName of a physical entity from the ConsensusPathDB database.CCAP strain numberbeta12orEarlierThe number of a strain of algae and protozoa from the CCAP database.Stock numberbeta12orEarlierAn identifier of stock from a catalogue of biological resources.Stock number (TAIR)A stock number from The Arabidopsis information resource (TAIR).beta12orEarlierREDIdb IDbeta12orEarlierIdentifier of an entry from the RNA editing database (REDIdb).SMART domain namebeta12orEarlierName of a domain from the SMART database.Protein family ID (PANTHER)Accession number of an entry (family) from the PANTHER database.beta12orEarlierPanther family IDRNAVirusDB IDbeta12orEarlierCould list (or reference) other taxa here from https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary.A unique identifier for a virus from the RNAVirusDB database.Virus IDAn accession of annotation on a (group of) viruses (catalogued in a database).beta12orEarlierNCBI Genome Project IDbeta12orEarlierAn identifier of a genome project assigned by NCBI.NCBI genome accessionA unique identifier of a whole genome assigned by the NCBI.beta12orEarlierSequence profile databeta12orEarliertrueData concerning, extracted from, or derived from the analysis of a sequence profile, such as its name, length, technical details about the profile or it's construction, the biological role or annotation, and so on.1.8Protein ID (TopDB)Unique identifier for a membrane protein from the TopDB database.TopDB IDbeta12orEarlierGel IDGel identifierbeta12orEarlierIdentifier of a two-dimensional (protein) gel.Reference map name (SWISS-2DPAGE)beta12orEarlierName of a reference map gel from the SWISS-2DPAGE database.Protein ID (PeroxiBase)beta12orEarlierPeroxiBase IDUnique identifier for a peroxidase protein from the PeroxiBase database.SISYPHUS IDIdentifier of an entry from the SISYPHUS database of tertiary structure alignments.beta12orEarlierORF IDbeta12orEarlierAccession of an open reading frame (catalogued in a database).ORF identifierbeta12orEarlierAn identifier of an open reading frame.Linucs IDIdentifier of an entry from the GlycosciencesDB database.beta12orEarlierProtein ID (LGICdb)beta12orEarlierLGICdb IDUnique identifier for a ligand-gated ion channel protein from the LGICdb database.MaizeDB IDIdentifier of an EST sequence from the MaizeDB database.beta12orEarlierGene ID (MfunGD)beta12orEarlierA unique identifier of gene in the MfunGD database.Orpha numberAn identifier of a disease from the Orpha database.beta12orEarlierProtein ID (EcID)Unique identifier for a protein from the EcID database.beta12orEarlierClone ID (RefSeq)A unique identifier of a cDNA molecule catalogued in the RefSeq database.beta12orEarlierProtein ID (ConoServer)beta12orEarlierUnique identifier for a cone snail toxin protein from the ConoServer database.GeneSNP IDIdentifier of a GeneSNP database entry.beta12orEarlierLipid identifierbeta12orEarlierIdentifier of a lipid.DatabankA flat-file (textual) data archive.beta12orEarliertruebeta12orEarlierWeb portalbeta12orEarliertruebeta12orEarlierA web site providing data (web pages) on a common theme to a HTTP client.Gene ID (VBASE2)VBASE2 IDbeta12orEarlierIdentifier for a gene from the VBASE2 database.DPVweb IDDPVweb virus IDA unique identifier for a virus from the DPVweb database.beta12orEarlierPathway ID (BioSystems)beta12orEarlier[0-9]+Identifier of a pathway from the BioSystems pathway database.Experimental data (proteomics)Data concerning a proteomics experiment.beta12orEarlierbeta12orEarliertrueAbstractAn abstract of a scientific article.beta12orEarlierLipid structurebeta12orEarlier3D coordinate and associated data for a lipid structure.Drug structure3D coordinate and associated data for the (3D) structure of a drug.beta12orEarlierToxin structurebeta12orEarlier3D coordinate and associated data for the (3D) structure of a toxin.Position-specific scoring matrixA simple matrix of numbers, where each value (or column of values) is derived derived from analysis of the corresponding position in a sequence alignment.beta12orEarlierPSSMDistance matrixA matrix of distances between molecular entities, where a value (distance) is (typically) derived from comparison of two entities and reflects their similarity.beta12orEarlierStructural distance matrixbeta12orEarlierDistances (values representing similarity) between a group of molecular structures.Article metadata1.5Bibliographic data concerning scientific article(s).beta12orEarliertrueOntology conceptA concept from a biological ontology.This includes any fields from the concept definition such as concept name, definition, comments and so on.beta12orEarlierCodon usage biasA numerical measure of differences in the frequency of occurrence of synonymous codons in DNA sequences.beta12orEarlierNorthern blot report1.8Northern Blot experiments.truebeta12orEarlierNucleic acid features report (VNTR)beta12orEarliertruevariable number of tandem repeat (VNTR) polymorphism in a DNA sequence.1.8Nucleic acid features report (microsatellite)microsatellite polymorphism in a DNA sequence.1.8truebeta12orEarlierNucleic acid features report (RFLP)restriction fragment length polymorphisms (RFLP) in a DNA sequence.beta12orEarliertrue1.8Radiation hybrid mapThe radiation method can break very closely linked markers providing a more detailed map. Most genetic markers and subsequences may be located to a defined map position and with a more precise estimates of distance than a linkage map.A map showing distance between genetic markers estimated by radiation-induced breaks in a chromosome.RH mapbeta12orEarlierID listbeta12orEarlierA simple list of data identifiers (such as database accessions), possibly with additional basic information on the addressed data.Phylogenetic gene frequencies dataGene frequencies data that may be read during phylogenetic tree calculation.beta12orEarlierSequence set (polymorphic)beta13beta12orEarliertrueA set of sub-sequences displaying some type of polymorphism, typically indicating the sequence in which they occur, their position and other metadata.DRCAT resourceAn entry (resource) from the DRCAT bioinformatics resource catalogue.truebeta12orEarlier1.5Protein complex3D coordinate and associated data for a multi-protein complex; two or more polypeptides chains in a stable, functional association with one another.beta12orEarlierProtein structural motif3D coordinate and associated data for a protein (3D) structural motif; any group of contiguous or non-contiguous amino acid residues but typically those forming a feature with a structural or functional role.beta12orEarlierLipid reportAnnotation on or information derived from one or more specific lipid 3D structure(s).beta12orEarlierSecondary structure imagetruebeta12orEarlier1.4Image of one or more molecular secondary structures.Secondary structure report1.5An informative report on general information, properties or features of one or more molecular secondary structures.beta12orEarliertrueDNA featuresDNA sequence-specific feature annotation (not in a feature table).truebeta12orEarlierbeta12orEarlierRNA features reportbeta12orEarliertrue1.5Features concerning RNA or regions of DNA that encode an RNA molecule.PlotBiological data that has been plotted as a graph of some type.beta12orEarlierNucleic acid features report (polymorphism)truebeta12orEarlierDNA polymorphism.Protein sequence recordA protein sequence and associated metadata.beta12orEarlierSequence record (protein)Nucleic acid sequence recordbeta12orEarlierDNA sequence recordRNA sequence recordSequence record (nucleic acid)Nucleotide sequence recordA nucleic acid sequence and associated metadata.Protein sequence record (full)A protein sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database.1.8truebeta12orEarlierNucleic acid sequence record (full) 1.8beta12orEarliertrueA nucleic acid sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database.Biological model accessionbeta12orEarlierAccession of a mathematical model, typically an entry from a database.Cell type nameThe name of a type or group of cells.beta12orEarlierCell type accessionbeta12orEarlierAccession of a type or group of cells (catalogued in a database).Cell type IDCompound accessionbeta12orEarlierAccession of an entry from a database of chemicals.Small molecule accessionChemical compound accessionDrug accessionAccession of a drug.beta12orEarlierToxin nameName of a toxin.beta12orEarlierToxin accessionAccession of a toxin (catalogued in a database).beta12orEarlierMonosaccharide accessionbeta12orEarlierAccession of a monosaccharide (catalogued in a database).Drug nameCommon name of a drug.beta12orEarlierCarbohydrate accessionAccession of an entry from a database of carbohydrates.beta12orEarlierMolecule accessionAccession of a specific molecule (catalogued in a database).beta12orEarlierData resource definition accessionbeta12orEarlierAccession of a data definition (catalogued in a database).Genome accessionbeta12orEarlierAn accession of a particular genome (in a database).Map accessionAn accession of a map of a molecular sequence (deposited in a database).beta12orEarlierLipid accessionAccession of an entry from a database of lipids.beta12orEarlierPeptide IDAccession of a peptide deposited in a database.beta12orEarlierProtein accessionbeta12orEarlierAccession of a protein deposited in a database.Protein accessionsOrganism accessionAn accession of annotation on a (group of) organisms (catalogued in a database).beta12orEarlierOrganism nameMoby:BriefOccurrenceRecordMoby:FirstEpithetMoby:OrganismsLongNameThe name of an organism (or group of organisms).Moby:OrganismsShortNameMoby:OccurrenceRecordMoby:Organism_Namebeta12orEarlierMoby:InfraspecificEpithetProtein family accessionAccession of a protein family (that is deposited in a database).beta12orEarlierTranscription factor accessionAccession of an entry from a database of transcription factors or binding sites.beta12orEarlierStrain accessionIdentifier of a strain of an organism variant, typically a plant, virus or bacterium.beta12orEarlierVirus identifierbeta12orEarlierAn accession of annotation on a (group of) viruses (catalogued in a database).Sequence features metadatabeta12orEarlierMetadata on sequence features.Gramene identifierIdentifier of a Gramene database entry.beta12orEarlierDDBJ accessionbeta12orEarlierDDBJ IDDDBJ identifierDDBJ accession numberAn identifier of an entry from the DDBJ sequence database.ConsensusPathDB identifierAn identifier of an entity from the ConsensusPathDB database.beta12orEarlierSequence databeta12orEarliertrue1.8Data concerning, extracted from, or derived from the analysis of molecular sequence(s). This is a broad data type and is used a placeholder for other, more specific types.Codon usagebeta13truebeta12orEarlierThis is a broad data type and is used a placeholder for other, more specific types.Data concerning codon usage.Article reporttruebeta12orEarlierData derived from the analysis of a scientific text such as a full text article from a scientific journal.1.5Sequence reportAn informative report of information about molecular sequence(s), including basic information (metadata), and reports generated from molecular sequence analysis, including positional features and non-positional properties.beta12orEarlierSequence-derived reportProtein secondary structure reportbeta12orEarlierAn informative report about the properties or features of one or more protein secondary structures.Hopp and Woods plotbeta12orEarlierA Hopp and Woods plot of predicted antigenicity of a peptide or protein.Nucleic acid melting curveShows the proportion of nucleic acid which are double-stranded versus temperature.A melting curve of a double-stranded nucleic acid molecule (DNA or DNA/RNA).beta12orEarlierNucleic acid probability profileShows the probability of a base pair not being melted (i.e. remaining as double-stranded DNA) at a specified temperaturebeta12orEarlierA probability profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA).Nucleic acid temperature profileMelting mapPlots melting temperature versus base position.beta12orEarlierA temperature profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA).Gene regulatory network reportbeta12orEarliertrue1.8A report typically including a map (diagram) of a gene regulatory network.2D PAGE gel reportbeta12orEarliertrue1.8An informative report on a two-dimensional (2D PAGE) gel.Oligonucleotide probe sets annotation1.14General annotation on a set of oligonucleotide probes, such as the gene name with which the probe set is associated and which probes belong to the set.truebeta12orEarlierMicroarray imagetruebeta12orEarlierAn image from a microarray experiment which (typically) allows a visualisation of probe hybridisation and gene-expression data.1.5ImageImageImage databeta12orEarlierhttp://semanticscience.org/resource/SIO_000079Biological or biomedical data has been rendered into an image, typically for display on screen.http://semanticscience.org/resource/SIO_000081Sequence imageImage of a molecular sequence, possibly with sequence features or properties shown.beta12orEarlierProtein hydropathy dataProtein hydropathy reportA report on protein properties concerning hydropathy.beta12orEarlierWorkflow databeta13Data concerning a computational workflow.beta12orEarliertrueWorkflow1.5beta12orEarliertrueA computational workflow.Secondary structure dataData concerning molecular secondary structure data.beta13beta12orEarliertrueProtein sequence (raw)Raw sequence (protein)beta12orEarlierA raw protein sequence (string of characters).Raw protein sequenceNucleic acid sequence (raw)Nucleic acid raw sequenceA raw nucleic acid sequence.Nucleotide sequence (raw)beta12orEarlierRaw sequence (nucleic acid)Protein sequencebeta12orEarlierhttp://purl.org/biotop/biotop.owl#AminoAcidSequenceInformationProtein sequencesOne or more protein sequences, possibly with associated annotation.Nucleic acid sequenceNucleotide sequencehttp://purl.org/biotop/biotop.owl#NucleotideSequenceInformationNucleic acid sequencesbeta12orEarlierNucleotide sequencesDNA sequenceOne or more nucleic acid sequences, possibly with associated annotation.Reaction databeta12orEarlierThis is a broad data type and is used a placeholder for other, more specific types.Enzyme kinetics annotationData concerning a biochemical reaction, typically data and more general annotation on the kinetics of enzyme-catalysed reaction.Reaction annotationPeptide propertyPeptide dataData concerning small peptides.beta12orEarlierProtein classificationbeta12orEarlierThis is a broad data type and is used a placeholder for other, more specific types.An informative report concerning the classification of protein sequences or structures.Sequence motif dataThis is a broad data type and is used a placeholder for other, more specific types.1.8trueData concerning specific or conserved pattern in molecular sequences.beta12orEarlierSequence profile databeta13Data concerning models representing a (typically multiple) sequence alignment.beta12orEarliertrueThis is a broad data type and is used a placeholder for other, more specific types.Pathway or network datatruebeta12orEarlierbeta13Data concerning a specific biological pathway or network.Pathway or network reportAn informative report concerning or derived from the analysis of a biological pathway or network, such as a map (diagram) or annotation.beta12orEarlierNucleic acid thermodynamic dataA thermodynamic or kinetic property of a nucleic acid molecule.beta12orEarlierNucleic acid property (thermodynamic or kinetic)Nucleic acid thermodynamic propertyNucleic acid classificationThis is a broad data type and is used a placeholder for other, more specific types.Data concerning the classification of nucleic acid sequences or structures.beta12orEarlierClassification reportbeta12orEarliertrueThis can include an entire classification, components such as classifiers, assignments of entities to a classification and so on.A report on a classification of molecular sequences, structures or other entities.1.5Protein features report (key folding sites)beta12orEarliertruekey residues involved in protein folding.1.8Protein geometry reportbeta12orEarlierGeometry data for a protein structure, for example bond lengths, bond angles, torsion angles, chiralities, planaraties etc.Torsion angle dataProtein structure imageStructure image (protein)An image of protein structure.beta12orEarlierPhylogenetic character weightsbeta12orEarlierWeights for sequence positions or characters in phylogenetic analysis where zero is defined as unweighted.Annotation trackGenome trackGenomic trackbeta12orEarlierAnnotation of one particular positional feature on a biomolecular (typically genome) sequence, suitable for import and display in a genome browser.Genome annotation trackGenome-browser trackSequence annotation trackUniProt accessionSwiss-Prot entry accession[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}beta12orEarlierUniProt accession number